diff --git a/packages/babel-core/src/config/build-config-chain.js b/packages/babel-core/src/config/build-config-chain.js
index 78e97794cf..c5f738cc11 100644
--- a/packages/babel-core/src/config/build-config-chain.js
+++ b/packages/babel-core/src/config/build-config-chain.js
@@ -4,6 +4,12 @@ import { getEnv } from "./helpers/environment";
 import path from "path";
 import micromatch from "micromatch";
 import buildDebug from "debug";
+import {
+  validate,
+  type ValidatedOptions,
+  type PluginList,
+  type IgnoreList,
+} from "./options";
 
 const debug = buildDebug("babel:config:config-chain");
 
@@ -11,19 +17,19 @@ import { findConfigs, loadConfig, type ConfigFile } from "./loading/files";
 
 import { makeWeakCache, makeStrongCache } from "./caching";
 
-type ConfigItem = {
-  type: "options" | "arguments",
-  options: {},
-  dirname: string,
+export type ConfigItem = {
+  type: "arguments" | "env" | "file",
+  options: ValidatedOptions,
   alias: string,
+  dirname: string,
 };
 
 type ConfigPart =
   | {
       part: "config",
       config: ConfigItem,
-      ignore: ?Array<mixed>,
-      only: ?Array<mixed>,
+      ignore: ?IgnoreList,
+      only: ?IgnoreList,
       activeEnv: string | null,
     }
   | {
@@ -33,11 +39,9 @@ type ConfigPart =
       activeEnv: string | null,
     };
 
-export default function buildConfigChain(opts: {}): Array<ConfigItem> | null {
-  if (typeof opts.filename !== "string" && opts.filename != null) {
-    throw new Error(".filename must be a string, null, or undefined");
-  }
-
+export default function buildConfigChain(
+  opts: ValidatedOptions,
+): Array<ConfigItem> | null {
   const filename = opts.filename ? path.resolve(opts.filename) : null;
   const builder = new ConfigChainBuilder(
     filename ? new LoadedFile(filename) : null,
@@ -70,7 +74,11 @@ class ConfigChainBuilder {
     this.file = file;
   }
 
-  mergeConfigArguments(opts: {}, dirname: string, envKey: string) {
+  mergeConfigArguments(
+    opts: ValidatedOptions,
+    dirname: string,
+    envKey: string,
+  ) {
     flattenArgumentsOptionsParts(opts, dirname, envKey).forEach(part =>
       this._processConfigPart(part, envKey),
     );
@@ -117,43 +125,26 @@ class ConfigChainBuilder {
  * object identity preserved between calls so that they can be used for caching.
  */
 function flattenArgumentsOptionsParts(
-  opts: {},
+  opts: ValidatedOptions,
   dirname: string,
   envKey: string,
 ): Array<ConfigPart> {
+  const {
+    env,
+    plugins,
+    presets,
+    passPerPreset,
+    extends: extendsPath,
+    ...options
+  } = opts;
+
   const raw = [];
-
-  const env = typeof opts.env === "object" ? opts.env : null;
-  const plugins = Array.isArray(opts.plugins) ? opts.plugins : null;
-  const presets = Array.isArray(opts.presets) ? opts.presets : null;
-  const passPerPreset =
-    typeof opts.passPerPreset === "boolean" ? opts.passPerPreset : false;
-
   if (env) {
     raw.push(...flattenArgumentsEnvOptionsParts(env)(dirname)(envKey));
   }
 
-  const innerOpts = Object.assign({}, opts);
-  // If the env, plugins, and presets values on the object aren't arrays or
-  // objects, leave them in the base opts so that normal options validation
-  // will throw errors on them later.
-  if (env) delete innerOpts.env;
-  if (plugins) delete innerOpts.plugins;
-  if (presets) {
-    delete innerOpts.presets;
-    delete innerOpts.passPerPreset;
-  }
-  delete innerOpts.extends;
-
-  if (Object.keys(innerOpts).length > 0) {
-    raw.push(
-      ...flattenOptionsParts({
-        type: "arguments",
-        options: innerOpts,
-        alias: "base",
-        dirname,
-      }),
-    );
+  if (Object.keys(options).length > 0) {
+    raw.push(...flattenOptionsParts(buildArgumentsItem(options, dirname)));
   }
 
   if (plugins) {
@@ -161,14 +152,14 @@ function flattenArgumentsOptionsParts(
   }
   if (presets) {
     raw.push(
-      ...flattenArgumentsPresetsOptionsParts(presets)(passPerPreset)(dirname),
+      ...flattenArgumentsPresetsOptionsParts(presets)(!!passPerPreset)(dirname),
     );
   }
 
-  if (opts.extends != null) {
+  if (extendsPath != null) {
     raw.push(
       ...flattenOptionsParts(
-        buildArgumentsItem({ extends: opts.extends }, dirname),
+        buildArgumentsItem({ extends: extendsPath }, dirname),
       ),
     );
   }
@@ -181,7 +172,7 @@ function flattenArgumentsOptionsParts(
  * the object identity of the 'env' object.
  */
 const flattenArgumentsEnvOptionsParts = makeWeakCache((env: {}) => {
-  const options = { env };
+  const options: ValidatedOptions = { env };
 
   return makeStrongCache((dirname: string) =>
     flattenOptionsPartsLookup(buildArgumentsItem(options, dirname)),
@@ -193,8 +184,8 @@ const flattenArgumentsEnvOptionsParts = makeWeakCache((env: {}) => {
  * the object identity of the 'plugins' object.
  */
 const flattenArgumentsPluginsOptionsParts = makeWeakCache(
-  (plugins: Array<mixed>) => {
-    const options = { plugins };
+  (plugins: PluginList) => {
+    const options: ValidatedOptions = { plugins };
 
     return makeStrongCache((dirname: string) =>
       flattenOptionsParts(buildArgumentsItem(options, dirname)),
@@ -207,8 +198,8 @@ const flattenArgumentsPluginsOptionsParts = makeWeakCache(
  * the object identity of the 'presets' object.
  */
 const flattenArgumentsPresetsOptionsParts = makeWeakCache(
-  (presets: Array<mixed>) =>
-    makeStrongCache((passPerPreset: ?boolean) => {
+  (presets: PluginList) =>
+    makeStrongCache((passPerPreset: boolean) => {
       // The concept of passPerPreset is integrally tied to the preset list
       // so unfortunately we need to copy both values here, adding an extra
       // layer of caching functions.
@@ -220,7 +211,10 @@ const flattenArgumentsPresetsOptionsParts = makeWeakCache(
     }),
 );
 
-function buildArgumentsItem(options: {}, dirname: string): ConfigItem {
+function buildArgumentsItem(
+  options: ValidatedOptions,
+  dirname: string,
+): ConfigItem {
   return {
     type: "arguments",
     options,
@@ -236,8 +230,8 @@ function buildArgumentsItem(options: {}, dirname: string): ConfigItem {
  */
 const flattenFileOptionsParts = makeWeakCache((file: ConfigFile) => {
   return flattenOptionsPartsLookup({
-    type: "options",
-    options: file.options,
+    type: "file",
+    options: validate("file", file.options),
     alias: file.filepath,
     dirname: file.dirname,
   });
@@ -278,74 +272,37 @@ function flattenOptionsParts(
   config: ConfigItem,
   activeEnv: string | null = null,
 ): Array<ConfigPart> {
-  const { type, options: rawOpts, alias, dirname } = config;
-
-  if (rawOpts.ignore != null && !Array.isArray(rawOpts.ignore)) {
-    throw new Error(
-      `.ignore should be an array, ${JSON.stringify(rawOpts.ignore)} given`,
-    );
-  }
-  if (rawOpts.only != null && !Array.isArray(rawOpts.only)) {
-    throw new Error(
-      `.only should be an array, ${JSON.stringify(rawOpts.only)} given`,
-    );
-  }
-  const ignore = rawOpts.ignore || null;
-  const only = rawOpts.only || null;
+  const { options: rawOpts, alias, dirname } = config;
 
   const parts = [];
 
-  if (
-    rawOpts.env != null &&
-    (typeof rawOpts.env !== "object" || Array.isArray(rawOpts.env))
-  ) {
-    throw new Error(".env block must be an object, null, or undefined");
+  if (rawOpts.env) {
+    for (const envKey of Object.keys(rawOpts.env)) {
+      if (rawOpts.env[envKey]) {
+        parts.push(
+          ...flattenOptionsParts(
+            {
+              type: "env",
+              options: rawOpts.env[envKey],
+              alias: alias + `.env.${envKey}`,
+              dirname,
+            },
+            envKey,
+          ),
+        );
+      }
+    }
   }
 
-  const rawEnv = rawOpts.env || {};
-
-  Object.keys(rawEnv).forEach(envKey => {
-    const envOpts = rawEnv[envKey];
-
-    if (envOpts !== undefined && activeEnv !== null && activeEnv !== envKey) {
-      throw new Error(`Unreachable .env[${envKey}] block detected`);
-    }
-
-    if (
-      envOpts != null &&
-      (typeof envOpts !== "object" || Array.isArray(envOpts))
-    ) {
-      throw new Error(".env[...] block must be an object, null, or undefined");
-    }
-
-    if (envOpts) {
-      parts.push(
-        ...flattenOptionsParts(
-          {
-            type,
-            options: envOpts,
-            alias: alias + `.env.${envKey}`,
-            dirname,
-          },
-          envKey,
-        ),
-      );
-    }
-  });
-
   parts.push({
     part: "config",
     config,
-    ignore,
-    only,
+    ignore: rawOpts.ignore,
+    only: rawOpts.only,
     activeEnv,
   });
 
   if (rawOpts.extends != null) {
-    if (typeof rawOpts.extends !== "string") {
-      throw new Error(".extends must be a string");
-    }
-
     parts.push({
       part: "extends",
       path: rawOpts.extends,
@@ -372,8 +329,8 @@ class LoadedFile {
    * Tests if a filename should be ignored based on "ignore" and "only" options.
    */
   shouldIgnore(
-    ignore: ?Array<mixed>,
-    only: ?Array<mixed>,
+    ignore: ?IgnoreList,
+    only: ?IgnoreList,
     dirname: string,
   ): boolean {
     if (ignore) {
@@ -407,7 +364,7 @@ class LoadedFile {
    * Returns result of calling function with filename if pattern is a function.
    * Otherwise returns result of matching pattern Regex with filename.
    */
-  _matchesPatterns(patterns: Array<mixed>, dirname: string): boolean {
+  _matchesPatterns(patterns: IgnoreList, dirname: string): boolean {
     const res = [];
     const strings = [];
     const fns = [];
@@ -415,12 +372,7 @@ class LoadedFile {
     patterns.forEach(pattern => {
       if (typeof pattern === "string") strings.push(pattern);
       else if (typeof pattern === "function") fns.push(pattern);
-      else if (pattern instanceof RegExp) res.push(pattern);
-      else {
-        throw new Error(
-          "Patterns must be a string, function, or regular expression",
-        );
-      }
+      else res.push(pattern);
     });
 
     const filename = this.filename;
diff --git a/packages/babel-core/src/config/caching.js b/packages/babel-core/src/config/caching.js
index 052e2803c3..bd12bc31ac 100644
--- a/packages/babel-core/src/config/caching.js
+++ b/packages/babel-core/src/config/caching.js
@@ -31,7 +31,7 @@ export function makeStrongCache<ArgT, ResultT>(
  * configures its caching behavior. Cached values are stored weakly and the function argument must be
  * an object type.
  */
-export function makeWeakCache<ArgT: {} | Array<*>, ResultT>(
+export function makeWeakCache<ArgT: {} | Array<*> | $ReadOnlyArray<*>, ResultT>(
   handler: (ArgT, CacheConfigurator) => ResultT,
   autoPermacache?: boolean,
 ): ArgT => ResultT {
diff --git a/packages/babel-core/src/config/index.js b/packages/babel-core/src/config/index.js
index 2676d24047..8e458cdf7d 100644
--- a/packages/babel-core/src/config/index.js
+++ b/packages/babel-core/src/config/index.js
@@ -16,7 +16,7 @@ export type PluginPasses = Array<PluginPassList>;
  * Standard API for loading Babel configuration data. Not for public consumption.
  */
 export default function loadConfig(opts: mixed): ResolvedConfig | null {
-  if (opts != null && typeof opts !== "object") {
+  if (opts != null && (typeof opts !== "object" || Array.isArray(opts))) {
     throw new Error("Babel options must be an object, null, or undefined");
   }
 
diff --git a/packages/babel-core/src/config/option-assertions.js b/packages/babel-core/src/config/option-assertions.js
new file mode 100644
index 0000000000..12aa4460c6
--- /dev/null
+++ b/packages/babel-core/src/config/option-assertions.js
@@ -0,0 +1,174 @@
+// @flow
+
+import type {
+  IgnoreList,
+  IgnoreItem,
+  PluginList,
+  PluginItem,
+  PluginTarget,
+  SourceMapsOption,
+  SourceTypeOption,
+  CompactOption,
+  RootInputSourceMapOption,
+} from "./options";
+
+export function assertSourceMaps(key: string, value: mixed): ?SourceMapsOption {
+  if (
+    value != null &&
+    typeof value !== "boolean" &&
+    value !== "inline" &&
+    value !== "both"
+  ) {
+    throw new Error(
+      `.${key} must be a boolean, "inline", "both", null, or undefined`,
+    );
+  }
+  return value;
+}
+
+export function assertCompact(key: string, value: mixed): ?CompactOption {
+  if (value != null && typeof value !== "boolean" && value !== "auto") {
+    throw new Error(`.${key} must be a boolean, "auto", null, or undefined`);
+  }
+  return value;
+}
+
+export function assertSourceType(key: string, value: mixed): ?SourceTypeOption {
+  if (value != null && value !== "module" && value !== "script") {
+    throw new Error(`.${key} must be "module", "script", null, or undefined`);
+  }
+  return value;
+}
+
+export function assertInputSourceMap(
+  key: string,
+  value: mixed,
+): ?RootInputSourceMapOption {
+  if (
+    value != null &&
+    typeof value !== "boolean" &&
+    typeof value !== "object"
+  ) {
+    throw new Error(
+      ".inputSourceMap must be a boolean, object, null, or undefined",
+    );
+  }
+  return value;
+}
+
+export function assertString(key: string, value: mixed): ?string {
+  if (value != null && typeof value !== "string") {
+    throw new Error(`.${key} must be a string, null, or undefined`);
+  }
+  return value;
+}
+
+export function assertFunction(key: string, value: mixed): ?Function {
+  if (value != null && typeof value !== "function") {
+    throw new Error(`.${key} must be a function, null, or undefined`);
+  }
+  return value;
+}
+
+export function assertBoolean(key: string, value: mixed): ?boolean {
+  if (value != null && typeof value !== "boolean") {
+    throw new Error(`.${key} must be a boolean, null, or undefined`);
+  }
+  return value;
+}
+
+export function assertObject(key: string, value: mixed): ?{} {
+  if (value != null && (typeof value !== "object" || Array.isArray(value))) {
+    throw new Error(`.${key} must be an object, null, or undefined`);
+  }
+  return value;
+}
+
+export function assertIgnoreList(key: string, value: mixed): ?IgnoreList {
+  const arr = assertArray(key, value);
+  if (arr) {
+    arr.forEach((item, i) => assertIgnoreItem(key, i, item));
+  }
+  return (arr: any);
+}
+function assertIgnoreItem(
+  key: string,
+  index: number,
+  value: mixed,
+): IgnoreItem {
+  if (
+    typeof value !== "string" &&
+    typeof value !== "function" &&
+    !(value instanceof RegExp)
+  ) {
+    throw new Error(
+      `.${key}[${index}] must be an array of string/Funtion/RegExp values, or null, or undefined`,
+    );
+  }
+  return value;
+}
+
+export function assertPluginList(key: string, value: mixed): ?PluginList {
+  const arr = assertArray(key, value);
+  if (arr) {
+    // Loop instead of using `.map` in order to preserve object identity
+    // for plugin array for use during config chain processing.
+    arr.forEach((item, i) => assertPluginItem(key, i, item));
+  }
+  return (arr: any);
+}
+function assertPluginItem(
+  key: string,
+  index: number,
+  value: mixed,
+): PluginItem {
+  if (Array.isArray(value)) {
+    if (value.length === 0) {
+      throw new Error(`.${key}[${index}] must include an object`);
+    }
+    if (value.length > 2) {
+      throw new Error(`.${key}[${index}] may only be a two-tuple`);
+    }
+
+    assertPluginTarget(key, index, true, value[0]);
+
+    if (value.length === 2) {
+      const opts = value[1];
+      if (opts != null && (typeof opts !== "object" || Array.isArray(opts))) {
+        throw new Error(
+          `.${key}[${index}][1] must be an object, null, or undefined`,
+        );
+      }
+    }
+  } else {
+    assertPluginTarget(key, index, false, value);
+  }
+
+  return (value: any);
+}
+function assertPluginTarget(
+  key: string,
+  index: number,
+  inArray: boolean,
+  value: mixed,
+): PluginTarget {
+  if (
+    (typeof value !== "object" || !value) &&
+    typeof value !== "string" &&
+    typeof value !== "function"
+  ) {
+    throw new Error(
+      `.${key}[${index}]${inArray
+        ? `[0]`
+        : ""} must be a string, object, function`,
+    );
+  }
+  return value;
+}
+
+function assertArray(key: string, value: mixed): ?$ReadOnlyArray<mixed> {
+  if (value != null && !Array.isArray(value)) {
+    throw new Error(`.${key} must be an array, null, or undefined`);
+  }
+  return value;
+}
diff --git a/packages/babel-core/src/config/option-manager.js b/packages/babel-core/src/config/option-manager.js
index ae63a9ba92..8a4537a272 100644
--- a/packages/babel-core/src/config/option-manager.js
+++ b/packages/babel-core/src/config/option-manager.js
@@ -4,13 +4,13 @@ import * as context from "../index";
 import Plugin from "./plugin";
 import defaults from "lodash/defaults";
 import merge from "lodash/merge";
-import removed from "./removed";
-import buildConfigChain from "./build-config-chain";
+import buildConfigChain, { type ConfigItem } from "./build-config-chain";
 import path from "path";
 import traverse from "@babel/traverse";
 import clone from "lodash/clone";
 import { makeWeakCache } from "./caching";
 import { getEnv } from "./helpers/environment";
+import { validate, type ValidatedOptions, type PluginItem } from "./options";
 
 import {
   loadPlugin,
@@ -19,50 +19,14 @@ import {
   loadGenerator,
 } from "./loading/files";
 
-type MergeOptions = {
-  +type: "arguments" | "options" | "preset",
-  options: {},
-  alias: string,
-  dirname: string,
-};
-
-const optionNames = new Set([
-  "filename",
-  "filenameRelative",
-  "inputSourceMap",
-  "env",
-  "retainLines",
-  "highlightCode",
-  "presets",
-  "plugins",
-  "ignore",
-  "only",
-  "code",
-  "ast",
-  "extends",
-  "comments",
-  "shouldPrintComment",
-  "wrapPluginVisitorMethod",
-  "compact",
-  "minified",
-  "sourceMaps",
-  "sourceMapTarget",
-  "sourceFileName",
-  "sourceRoot",
-  "babelrc",
-  "sourceType",
-  "auxiliaryCommentBefore",
-  "auxiliaryCommentAfter",
-  "getModuleId",
-  "moduleRoot",
-  "moduleIds",
-  "moduleId",
-  "passPerPreset",
-  // Deprecate top level parserOpts
-  "parserOpts",
-  // Deprecate top level generatorOpts
-  "generatorOpts",
-]);
+type MergeOptions =
+  | ConfigItem
+  | {
+      type: "preset",
+      options: ValidatedOptions,
+      alias: string,
+      dirname: string,
+    };
 
 const ALLOWED_PLUGIN_KEYS = new Set([
   "name",
@@ -82,11 +46,11 @@ export default function manageOptions(opts: {}): {
 
 class OptionManager {
   constructor() {
-    this.options = createInitialOptions();
+    this.options = {};
     this.passes = [[]];
   }
 
-  options: Object;
+  options: ValidatedOptions;
   passes: Array<Array<Plugin>>;
 
   /**
@@ -108,12 +72,6 @@ class OptionManager {
       loadPresetDescriptor(descriptor),
     );
 
-    if (
-      config.options.passPerPreset != null &&
-      typeof config.options.passPerPreset !== "boolean"
-    ) {
-      throw new Error(".passPerPreset must be a boolean or undefined");
-    }
     const passPerPreset = config.options.passPerPreset;
     pass = pass || this.passes[0];
 
@@ -142,12 +100,22 @@ class OptionManager {
     delete options.env;
     delete options.plugins;
     delete options.presets;
+    delete options.passPerPreset;
+
+    // "sourceMap" is just aliased to sourceMap, so copy it over as
+    // we merge the options together.
+    if (options.sourceMap) {
+      options.sourceMaps = options.sourceMap;
+      delete options.sourceMap;
+    }
 
     merge(this.options, options);
   }
 
-  init(opts: {}) {
-    const configChain = buildConfigChain(opts);
+  init(inputOpts: {}) {
+    const args = validate("arguments", inputOpts);
+
+    const configChain = buildConfigChain(args);
     if (!configChain) return null;
 
     try {
@@ -158,15 +126,13 @@ class OptionManager {
       // There are a few case where thrown errors will try to annotate themselves multiple times, so
       // to keep things simple we just bail out if re-wrapping the message.
       if (!/^\[BABEL\]/.test(e.message)) {
-        const filename =
-          typeof opts.filename === "string" ? opts.filename : null;
-        e.message = `[BABEL] ${filename || "unknown"}: ${e.message}`;
+        e.message = `[BABEL] ${args.filename || "unknown"}: ${e.message}`;
       }
 
       throw e;
     }
 
-    opts = this.options;
+    const opts: Object = merge(createInitialOptions(), this.options);
 
     // Tack the passes onto the object itself so that, if this object is passed back to Babel a second time,
     // it will be in the right structure to not change behavior.
@@ -175,6 +141,7 @@ class OptionManager {
       .slice(1)
       .filter(plugins => plugins.length > 0)
       .map(plugins => ({ plugins }));
+    opts.passPerPreset = opts.presets.length > 0;
 
     if (opts.inputSourceMap) {
       opts.sourceMaps = true;
@@ -231,20 +198,13 @@ type LoadedDescriptor = {
 /**
  * Load and validate the given config into a set of options, plugins, and presets.
  */
-const loadConfig = makeWeakCache((config): {
+const loadConfig = makeWeakCache((config: MergeOptions): {
   options: {},
   plugins: Array<BasicDescriptor>,
   presets: Array<BasicDescriptor>,
 } => {
   const options = normalizeOptions(config);
 
-  if (
-    config.options.plugins != null &&
-    !Array.isArray(config.options.plugins)
-  ) {
-    throw new Error(".plugins should be an array, null, or undefined");
-  }
-
   const plugins = (config.options.plugins || []).map((plugin, index) => {
     const { filepath, value, options } = normalizePair(
       plugin,
@@ -260,13 +220,6 @@ const loadConfig = makeWeakCache((config): {
     };
   });
 
-  if (
-    config.options.presets != null &&
-    !Array.isArray(config.options.presets)
-  ) {
-    throw new Error(".presets should be an array, null, or undefined");
-  }
-
   const presets = (config.options.presets || []).map((preset, index) => {
     const { filepath, value, options } = normalizePair(
       preset,
@@ -405,7 +358,7 @@ const instantiatePreset = makeWeakCache(
   ({ value, dirname, alias }: LoadedDescriptor): MergeOptions => {
     return {
       type: "preset",
-      options: value,
+      options: validate("preset", value),
       alias,
       dirname,
     };
@@ -416,72 +369,12 @@ const instantiatePreset = makeWeakCache(
  * Validate and return the options object for the config.
  */
 function normalizeOptions(config) {
-  const alias = config.alias || "foreign";
-  const type = config.type;
-
-  //
-  if (typeof config.options !== "object" || Array.isArray(config.options)) {
-    throw new TypeError(`Invalid options type for ${alias}`);
-  }
-
   //
   const options = Object.assign({}, config.options);
 
-  if (type !== "arguments") {
-    if (options.filename !== undefined) {
-      throw new Error(`${alias}.filename is only allowed as a root argument`);
-    }
-
-    if (options.babelrc !== undefined) {
-      throw new Error(`${alias}.babelrc is only allowed as a root argument`);
-    }
-  }
-
-  if (type === "preset") {
-    if (options.only !== undefined) {
-      throw new Error(`${alias}.only is not supported in a preset`);
-    }
-    if (options.ignore !== undefined) {
-      throw new Error(`${alias}.ignore is not supported in a preset`);
-    }
-    if (options.extends !== undefined) {
-      throw new Error(`${alias}.extends is not supported in a preset`);
-    }
-    if (options.env !== undefined) {
-      throw new Error(`${alias}.env is not supported in a preset`);
-    }
-  }
-
-  if (options.sourceMap !== undefined) {
-    if (options.sourceMaps !== undefined) {
-      throw new Error(`Both ${alias}.sourceMap and .sourceMaps have been set`);
-    }
-
-    options.sourceMaps = options.sourceMap;
-    delete options.sourceMap;
-  }
-
-  for (const key in options) {
-    // check for an unknown option
-    if (!optionNames.has(key)) {
-      if (removed[key]) {
-        const { message, version = 5 } = removed[key];
-
-        throw new ReferenceError(
-          `Using removed Babel ${version} option: ${alias}.${key} - ${message}`,
-        );
-      } else {
-        // eslint-disable-next-line max-len
-        const unknownOptErr = `Unknown option: ${alias}.${key}. Check out http://babeljs.io/docs/usage/options/ for more information about options.`;
-
-        throw new ReferenceError(unknownOptErr);
-      }
-    }
-  }
-
   if (options.parserOpts && typeof options.parserOpts.parser === "string") {
     options.parserOpts = Object.assign({}, options.parserOpts);
-    options.parserOpts.parser = loadParser(
+    (options.parserOpts: any).parser = loadParser(
       options.parserOpts.parser,
       config.dirname,
     ).value;
@@ -492,16 +385,12 @@ function normalizeOptions(config) {
     typeof options.generatorOpts.generator === "string"
   ) {
     options.generatorOpts = Object.assign({}, options.generatorOpts);
-    options.generatorOpts.generator = loadGenerator(
+    (options.generatorOpts: any).generator = loadGenerator(
       options.generatorOpts.generator,
       config.dirname,
     ).value;
   }
 
-  delete options.passPerPreset;
-  delete options.plugins;
-  delete options.presets;
-
   return options;
 }
 
@@ -509,7 +398,7 @@ function normalizeOptions(config) {
  * Given a plugin/preset item, resolve it into a standard format.
  */
 function normalizePair(
-  pair: mixed,
+  pair: PluginItem,
   resolver,
   dirname,
 ): {
@@ -519,14 +408,8 @@ function normalizePair(
 } {
   let options;
   let value = pair;
-  if (Array.isArray(pair)) {
-    if (pair.length > 2) {
-      throw new Error(
-        `Unexpected extra options ${JSON.stringify(pair.slice(2))}.`,
-      );
-    }
-
-    [value, options] = pair;
+  if (Array.isArray(value)) {
+    [value, options] = value;
   }
 
   let filepath = null;
diff --git a/packages/babel-core/src/config/options.js b/packages/babel-core/src/config/options.js
new file mode 100644
index 0000000000..75a91388f9
--- /dev/null
+++ b/packages/babel-core/src/config/options.js
@@ -0,0 +1,255 @@
+// @flow
+
+import removed from "./removed";
+import {
+  assertString,
+  assertBoolean,
+  assertObject,
+  assertInputSourceMap,
+  assertIgnoreList,
+  assertPluginList,
+  assertFunction,
+  assertSourceMaps,
+  assertCompact,
+  assertSourceType,
+} from "./option-assertions";
+
+type ValidatorSet = {
+  [string]: Validator<any>,
+};
+
+type Validator<T> = (string, mixed) => T;
+
+const ROOT_VALIDATORS: ValidatorSet = {
+  filename: (assertString: Validator<
+    $PropertyType<ValidatedOptions, "filename">,
+  >),
+  filenameRelative: (assertString: Validator<
+    $PropertyType<ValidatedOptions, "filenameRelative">,
+  >),
+  babelrc: (assertBoolean: Validator<
+    $PropertyType<ValidatedOptions, "babelrc">,
+  >),
+  code: (assertBoolean: Validator<$PropertyType<ValidatedOptions, "code">>),
+  ast: (assertBoolean: Validator<$PropertyType<ValidatedOptions, "ast">>),
+};
+
+const NONPRESET_VALIDATORS: ValidatorSet = {
+  extends: (assertString: Validator<
+    $PropertyType<ValidatedOptions, "extends">,
+  >),
+  env: (assertEnvSet: Validator<$PropertyType<ValidatedOptions, "env">>),
+  ignore: (assertIgnoreList: Validator<
+    $PropertyType<ValidatedOptions, "ignore">,
+  >),
+  only: (assertIgnoreList: Validator<$PropertyType<ValidatedOptions, "only">>),
+};
+
+const COMMON_VALIDATORS: ValidatorSet = {
+  // TODO: Should 'inputSourceMap' be moved to be a root-only option?
+  // We may want a boolean-only version to be a common option, with the
+  // object only allowed as a root config argument.
+  inputSourceMap: (assertInputSourceMap: Validator<
+    $PropertyType<ValidatedOptions, "inputSourceMap">,
+  >),
+  presets: (assertPluginList: Validator<
+    $PropertyType<ValidatedOptions, "presets">,
+  >),
+  plugins: (assertPluginList: Validator<
+    $PropertyType<ValidatedOptions, "plugins">,
+  >),
+  passPerPreset: (assertBoolean: Validator<
+    $PropertyType<ValidatedOptions, "passPerPreset">,
+  >),
+  retainLines: (assertBoolean: Validator<
+    $PropertyType<ValidatedOptions, "retainLines">,
+  >),
+  comments: (assertBoolean: Validator<
+    $PropertyType<ValidatedOptions, "comments">,
+  >),
+  shouldPrintComment: (assertFunction: Validator<
+    $PropertyType<ValidatedOptions, "shouldPrintComment">,
+  >),
+  compact: (assertCompact: Validator<
+    $PropertyType<ValidatedOptions, "compact">,
+  >),
+  minified: (assertBoolean: Validator<
+    $PropertyType<ValidatedOptions, "minified">,
+  >),
+  auxiliaryCommentBefore: (assertString: Validator<
+    $PropertyType<ValidatedOptions, "auxiliaryCommentBefore">,
+  >),
+  auxiliaryCommentAfter: (assertString: Validator<
+    $PropertyType<ValidatedOptions, "auxiliaryCommentAfter">,
+  >),
+  sourceType: (assertSourceType: Validator<
+    $PropertyType<ValidatedOptions, "sourceType">,
+  >),
+  wrapPluginVisitorMethod: (assertFunction: Validator<
+    $PropertyType<ValidatedOptions, "wrapPluginVisitorMethod">,
+  >),
+  highlightCode: (assertBoolean: Validator<
+    $PropertyType<ValidatedOptions, "highlightCode">,
+  >),
+  sourceMaps: (assertSourceMaps: Validator<
+    $PropertyType<ValidatedOptions, "sourceMaps">,
+  >),
+  sourceMap: (assertSourceMaps: Validator<
+    $PropertyType<ValidatedOptions, "sourceMap">,
+  >),
+  sourceMapTarget: (assertString: Validator<
+    $PropertyType<ValidatedOptions, "sourceMapTarget">,
+  >),
+  sourceFileName: (assertString: Validator<
+    $PropertyType<ValidatedOptions, "sourceFileName">,
+  >),
+  sourceRoot: (assertString: Validator<
+    $PropertyType<ValidatedOptions, "sourceRoot">,
+  >),
+  getModuleId: (assertFunction: Validator<
+    $PropertyType<ValidatedOptions, "getModuleId">,
+  >),
+  moduleRoot: (assertString: Validator<
+    $PropertyType<ValidatedOptions, "moduleRoot">,
+  >),
+  moduleIds: (assertBoolean: Validator<
+    $PropertyType<ValidatedOptions, "moduleIds">,
+  >),
+  moduleId: (assertString: Validator<
+    $PropertyType<ValidatedOptions, "moduleId">,
+  >),
+  parserOpts: (assertObject: Validator<
+    $PropertyType<ValidatedOptions, "parserOpts">,
+  >),
+  generatorOpts: (assertObject: Validator<
+    $PropertyType<ValidatedOptions, "generatorOpts">,
+  >),
+};
+export type ValidatedOptions = {
+  filename?: ?string,
+  filenameRelative?: ?string,
+  babelrc?: ?boolean,
+  code?: ?boolean,
+  ast?: ?boolean,
+  inputSourceMap?: ?RootInputSourceMapOption,
+
+  extends?: ?string,
+  env?: ?EnvSet<ValidatedOptions>,
+  ignore?: ?IgnoreList,
+  only?: ?IgnoreList,
+
+  presets?: ?PluginList,
+  plugins?: ?PluginList,
+  passPerPreset?: ?boolean,
+
+  // Options for @babel/generator
+  retainLines?: ?boolean,
+  comments?: ?boolean,
+  shouldPrintComment?: ?Function,
+  compact?: ?CompactOption,
+  minified?: ?boolean,
+  auxiliaryCommentBefore?: ?string,
+  auxiliaryCommentAfter?: ?string,
+
+  // Parser
+  sourceType?: ?SourceTypeOption,
+
+  wrapPluginVisitorMethod?: ?Function,
+  highlightCode?: ?boolean,
+
+  // Sourcemap generation options.
+  sourceMaps?: ?SourceMapsOption,
+  sourceMap?: ?SourceMapsOption,
+  sourceMapTarget?: ?string,
+  sourceFileName?: ?string,
+  sourceRoot?: ?string,
+
+  // AMD/UMD/SystemJS module naming options.
+  getModuleId?: ?Function,
+  moduleRoot?: ?string,
+  moduleIds?: ?boolean,
+  moduleId?: ?string,
+
+  // Deprecate top level parserOpts
+  parserOpts?: ?{},
+  // Deprecate top level generatorOpts
+  generatorOpts?: ?{},
+};
+
+export type EnvSet<T> = {
+  [string]: ?T,
+};
+export type IgnoreItem = string | Function | RegExp;
+export type IgnoreList = $ReadOnlyArray<IgnoreItem>;
+
+export type PluginTarget = string | {} | Function;
+export type PluginItem = PluginTarget | [PluginTarget, {} | void];
+export type PluginList = $ReadOnlyArray<PluginItem>;
+
+export type SourceMapsOption = boolean | "inline" | "both";
+export type SourceTypeOption = "module" | "script";
+export type CompactOption = boolean | "auto";
+export type RootInputSourceMapOption = {} | boolean;
+
+export type OptionsType = "arguments" | "file" | "env" | "preset";
+
+export function validate(type: OptionsType, opts: {}): ValidatedOptions {
+  assertNoDuplicateSourcemap(opts);
+
+  Object.keys(opts).forEach(key => {
+    if (type === "preset" && NONPRESET_VALIDATORS[key]) {
+      throw new Error(`.${key} is not allowed in preset options`);
+    }
+    if (type !== "arguments" && ROOT_VALIDATORS[key]) {
+      throw new Error(`.${key} is only allowed in root programmatic options`);
+    }
+
+    const validator =
+      COMMON_VALIDATORS[key] ||
+      NONPRESET_VALIDATORS[key] ||
+      ROOT_VALIDATORS[key];
+
+    if (validator) validator(key, opts[key]);
+    else throw buildUnknownError(key);
+  });
+
+  return (opts: any);
+}
+
+function buildUnknownError(key: string) {
+  if (removed[key]) {
+    const { message, version = 5 } = removed[key];
+
+    throw new ReferenceError(
+      `Using removed Babel ${version} option: .${key} - ${message}`,
+    );
+  } else {
+    // eslint-disable-next-line max-len
+    const unknownOptErr = `Unknown option: .${key}. Check out http://babeljs.io/docs/usage/options/ for more information about options.`;
+
+    throw new ReferenceError(unknownOptErr);
+  }
+}
+
+function has(obj: {}, key: string) {
+  return Object.prototype.hasOwnProperty.call(obj, key);
+}
+
+function assertNoDuplicateSourcemap(opts: {}): void {
+  if (has(opts, "sourceMap") && has(opts, "sourceMaps")) {
+    throw new Error(".sourceMap is an alias for .sourceMaps, cannot use both");
+  }
+}
+
+function assertEnvSet(key: string, value: mixed): ?EnvSet<ValidatedOptions> {
+  const obj = assertObject(key, value);
+  if (obj) {
+    // Validate but don't copy the .env object in order to preserve
+    // object identity for use during config chain processing.
+    for (const key of Object.keys(obj)) {
+      const env = assertObject(key, obj[key]);
+      if (env) validate("env", env);
+    }
+  }
+  return (obj: any);
+}
diff --git a/packages/babel-core/test/api.js b/packages/babel-core/test/api.js
index e66d88d6cf..cad0308862 100644
--- a/packages/babel-core/test/api.js
+++ b/packages/babel-core/test/api.js
@@ -145,7 +145,7 @@ describe("api", function() {
       babel.transform("", {
         plugins: [__dirname + "/../../babel-plugin-syntax-jsx", false],
       });
-    }, /Error: \[BABEL\] unknown: Unexpected falsy value: false/);
+    }, /.plugins\[1\] must be a string, object, function/);
   });
 
   it("options merge backwards", function() {
diff --git a/packages/babel-core/test/config-chain.js b/packages/babel-core/test/config-chain.js
index e004a8aaa2..097112cb07 100644
--- a/packages/babel-core/test/config-chain.js
+++ b/packages/babel-core/test/config-chain.js
@@ -372,7 +372,7 @@ describe("buildConfigChain", function() {
 
     const expected = [
       {
-        type: "options",
+        type: "file",
         options: {
           plugins: ["extended"],
         },
@@ -380,7 +380,7 @@ describe("buildConfigChain", function() {
         dirname: fixture(),
       },
       {
-        type: "options",
+        type: "file",
         options: {
           extends: "./extended.babelrc.json",
           plugins: ["root"],
@@ -389,7 +389,7 @@ describe("buildConfigChain", function() {
         dirname: fixture(),
       },
       {
-        type: "options",
+        type: "file",
         options: {
           ignore: ["root-ignore"],
         },
@@ -416,7 +416,7 @@ describe("buildConfigChain", function() {
 
     const expected = [
       {
-        type: "options",
+        type: "file",
         options: {
           ignore: ["root-ignore"],
         },
@@ -424,7 +424,7 @@ describe("buildConfigChain", function() {
         dirname: fixture(),
       },
       {
-        type: "options",
+        type: "file",
         options: {
           plugins: ["dir2"],
         },
@@ -451,7 +451,7 @@ describe("buildConfigChain", function() {
 
     const expected = [
       {
-        type: "options",
+        type: "file",
         options: {
           plugins: ["extended"],
         },
@@ -459,7 +459,7 @@ describe("buildConfigChain", function() {
         dirname: fixture(),
       },
       {
-        type: "options",
+        type: "file",
         options: {
           extends: "./extended.babelrc.json",
           plugins: ["root"],
@@ -468,7 +468,7 @@ describe("buildConfigChain", function() {
         dirname: fixture(),
       },
       {
-        type: "options",
+        type: "file",
         options: {
           ignore: ["root-ignore"],
         },
@@ -495,7 +495,7 @@ describe("buildConfigChain", function() {
 
     const expected = [
       {
-        type: "options",
+        type: "file",
         options: {
           ignore: ["root-ignore"],
         },
@@ -503,7 +503,7 @@ describe("buildConfigChain", function() {
         dirname: fixture(),
       },
       {
-        type: "options",
+        type: "file",
         options: {
           env: {
             bar: {
@@ -540,7 +540,7 @@ describe("buildConfigChain", function() {
 
     const expected = [
       {
-        type: "options",
+        type: "file",
         options: {
           ignore: ["root-ignore"],
         },
@@ -548,7 +548,7 @@ describe("buildConfigChain", function() {
         dirname: fixture(),
       },
       {
-        type: "options",
+        type: "file",
         options: {
           env: {
             bar: {
@@ -564,7 +564,7 @@ describe("buildConfigChain", function() {
         dirname: fixture("env"),
       },
       {
-        type: "options",
+        type: "env",
         options: {
           plugins: ["env-foo"],
         },
@@ -594,7 +594,7 @@ describe("buildConfigChain", function() {
 
     const expected = [
       {
-        type: "options",
+        type: "file",
         options: {
           ignore: ["root-ignore"],
         },
@@ -602,7 +602,7 @@ describe("buildConfigChain", function() {
         dirname: fixture(),
       },
       {
-        type: "options",
+        type: "file",
         options: {
           env: {
             bar: {
@@ -618,7 +618,7 @@ describe("buildConfigChain", function() {
         dirname: fixture("env"),
       },
       {
-        type: "options",
+        type: "env",
         options: {
           plugins: ["env-bar"],
         },
@@ -647,7 +647,7 @@ describe("buildConfigChain", function() {
 
     const expected = [
       {
-        type: "options",
+        type: "file",
         options: {
           plugins: ["pkg-plugin"],
         },
@@ -655,7 +655,7 @@ describe("buildConfigChain", function() {
         dirname: fixture("pkg"),
       },
       {
-        type: "options",
+        type: "file",
         options: {
           ignore: ["pkg-ignore"],
         },
@@ -682,7 +682,7 @@ describe("buildConfigChain", function() {
 
     const expected = [
       {
-        type: "options",
+        type: "file",
         options: {
           ignore: ["root-ignore"],
         },
@@ -690,7 +690,7 @@ describe("buildConfigChain", function() {
         dirname: fixture(),
       },
       {
-        type: "options",
+        type: "file",
         options: {
           plugins: ["foo", "bar"],
         },
@@ -717,7 +717,7 @@ describe("buildConfigChain", function() {
 
     const expected = [
       {
-        type: "options",
+        type: "file",
         options: {
           ignore: ["root-ignore"],
         },
@@ -725,7 +725,7 @@ describe("buildConfigChain", function() {
         dirname: fixture(),
       },
       {
-        type: "options",
+        type: "file",
         options: {
           compact: true,
         },
@@ -752,7 +752,7 @@ describe("buildConfigChain", function() {
 
     const expected = [
       {
-        type: "options",
+        type: "file",
         options: {
           ignore: ["root-ignore"],
         },
@@ -760,7 +760,7 @@ describe("buildConfigChain", function() {
         dirname: fixture(),
       },
       {
-        type: "options",
+        type: "file",
         options: {
           plugins: ["foo", "bar"],
         },
@@ -786,7 +786,7 @@ describe("buildConfigChain", function() {
 
     const expected = [
       {
-        type: "options",
+        type: "file",
         options: {
           ignore: ["root-ignore"],
         },
@@ -794,7 +794,7 @@ describe("buildConfigChain", function() {
         dirname: fixture(),
       },
       {
-        type: "options",
+        type: "file",
         options: {
           plugins: ["extended"],
         },
@@ -802,7 +802,7 @@ describe("buildConfigChain", function() {
         dirname: fixture(),
       },
       {
-        type: "options",
+        type: "file",
         options: {
           extends: "../extended.babelrc.json",
           plugins: ["foo", "bar"],
@@ -833,7 +833,7 @@ describe("buildConfigChain", function() {
 
       const expected = [
         {
-          type: "options",
+          type: "file",
           options: {
             ignore: ["root-ignore"],
           },
@@ -841,7 +841,7 @@ describe("buildConfigChain", function() {
           dirname: fixture(),
         },
         {
-          type: "options",
+          type: "file",
           options: {
             plugins: ["json"],
           },
@@ -869,7 +869,7 @@ describe("buildConfigChain", function() {
 
     const expected = [
       {
-        type: "options",
+        type: "file",
         options: {
           ignore: ["root-ignore"],
         },
@@ -877,7 +877,7 @@ describe("buildConfigChain", function() {
         dirname: fixture(),
       },
       {
-        type: "options",
+        type: "file",
         options: {
           ignore: ["*", "!src.js"],
         },
@@ -910,7 +910,7 @@ describe("buildConfigChain", function() {
 
     const expected = [
       {
-        type: "options",
+        type: "file",
         options: {
           ignore: ["root-ignore"],
         },
@@ -918,7 +918,7 @@ describe("buildConfigChain", function() {
         dirname: fixture(),
       },
       {
-        type: "options",
+        type: "file",
         options: {
           ignore: ["*", "!folder"],
         },
diff --git a/packages/babel-core/test/option-manager.js b/packages/babel-core/test/option-manager.js
index 7e233a2a67..f6429615f5 100644
--- a/packages/babel-core/test/option-manager.js
+++ b/packages/babel-core/test/option-manager.js
@@ -17,7 +17,7 @@ describe("option-manager", () => {
         manageOptions({
           randomOption: true,
         });
-      }, /Unknown option: base.randomOption/);
+      }, /Unknown option: .randomOption/);
     });
 
     it("throws for removed babel 5 options", () => {
@@ -29,7 +29,7 @@ describe("option-manager", () => {
           });
         },
         // eslint-disable-next-line max-len
-        /Using removed Babel 5 option: base.auxiliaryComment - Use `auxiliaryCommentBefore` or `auxiliaryCommentAfter`/,
+        /Using removed Babel 5 option: .auxiliaryComment - Use `auxiliaryCommentBefore` or `auxiliaryCommentAfter`/,
       );
     });
 
@@ -47,7 +47,7 @@ describe("option-manager", () => {
   describe("source type", function() {
     it("should set module for .mjs extension", () => {
       const config = manageOptions({
-        sourceType: "program",
+        sourceType: "script",
         filename: "foo.mjs",
       });