diff --git a/packages/babel-cli/src/babel/index.js b/packages/babel-cli/src/babel/index.js
index 48682c11fa..696c42fe18 100755
--- a/packages/babel-cli/src/babel/index.js
+++ b/packages/babel-cli/src/babel/index.js
@@ -238,10 +238,6 @@ if (errors.length) {
 //
 
 const opts = commander.opts();
-//the configFile CLI option maps to the extends option in the node API
-if (opts.configFile) {
-  opts.extends = opts.configFile;
-}
 
 // Delete options that are specific to @babel/cli and shouldn't be passed to @babel/core.
 delete opts.version;
@@ -253,7 +249,6 @@ delete opts.outDir;
 delete opts.copyFiles;
 delete opts.includeDotfiles;
 delete opts.verbose;
-delete opts.configFile;
 delete opts.deleteDirOnStart;
 delete opts.keepFileExtension;
 delete opts.relative;
diff --git a/packages/babel-core/src/config/config-chain.js b/packages/babel-core/src/config/config-chain.js
index 2ca2a5c3bf..ef607ccdd0 100644
--- a/packages/babel-core/src/config/config-chain.js
+++ b/packages/babel-core/src/config/config-chain.js
@@ -15,6 +15,7 @@ const debug = buildDebug("babel:config:config-chain");
 import {
   findPackageData,
   findRelativeConfig,
+  findRootConfig,
   loadConfig,
   type ConfigFile,
   type IgnoreFile,
@@ -107,6 +108,7 @@ const loadPresetOverridesEnvDescriptors = makeWeakCache(
 
 export type RootConfigChain = ConfigChain & {
   babelrc: ConfigFile | void,
+  config: ConfigFile | void,
   ignore: IgnoreFile | void,
 };
 
@@ -126,6 +128,26 @@ export function buildRootChain(
   );
   if (!programmaticChain) return null;
 
+  const { root: rootDir = ".", configFile: configFileName } = opts;
+
+  let configFile;
+  if (typeof configFileName === "string") {
+    configFile = loadConfig(configFileName, context.cwd, context.envName);
+  } else if (configFileName === undefined || configFileName === true) {
+    configFile = findRootConfig(
+      path.resolve(context.cwd, rootDir),
+      context.envName,
+    );
+  }
+
+  const configFileChain = emptyChain();
+  if (configFile) {
+    const result = loadFileChain(configFile, context);
+    if (!result) return null;
+
+    mergeChain(configFileChain, result);
+  }
+
   const pkgData =
     typeof context.filename === "string"
       ? findPackageData(context.filename)
@@ -155,7 +177,7 @@ export function buildRootChain(
   // Insert file chain in front so programmatic options have priority
   // over configuration file chain items.
   const chain = mergeChain(
-    mergeChain(emptyChain(), fileChain),
+    mergeChain(mergeChain(emptyChain(), configFileChain), fileChain),
     programmaticChain,
   );
 
@@ -165,6 +187,7 @@ export function buildRootChain(
     options: chain.options.map(o => normalizeOptions(o)),
     ignore: ignore || undefined,
     babelrc: babelrc || undefined,
+    config: configFile || undefined,
   };
 }
 
diff --git a/packages/babel-core/src/config/files/configuration.js b/packages/babel-core/src/config/files/configuration.js
index ccc300ae48..e7022ce2bc 100644
--- a/packages/babel-core/src/config/files/configuration.js
+++ b/packages/babel-core/src/config/files/configuration.js
@@ -16,6 +16,8 @@ import type { FilePackageData, RelativeConfig, ConfigFile } from "./types";
 
 const debug = buildDebug("babel:config:loading:files:configuration");
 
+const BABEL_CONFIG_JS_FILENAME = "babel.config.js";
+
 const BABELRC_FILENAME = ".babelrc";
 const BABELRC_JS_FILENAME = ".babelrc.js";
 const BABELIGNORE_FILENAME = ".babelignore";
@@ -85,6 +87,19 @@ export function findRelativeConfig(
   return { config, ignore };
 }
 
+export function findRootConfig(
+  dirname: string,
+  envName: string,
+): ConfigFile | null {
+  const filepath = path.resolve(dirname, BABEL_CONFIG_JS_FILENAME);
+
+  const conf = readConfig(filepath, envName);
+  if (conf) {
+    debug("Found root config %o in $o.", BABEL_CONFIG_JS_FILENAME, dirname);
+  }
+  return conf;
+}
+
 export function loadConfig(
   name: string,
   dirname: string,
diff --git a/packages/babel-core/src/config/files/index-browser.js b/packages/babel-core/src/config/files/index-browser.js
index 9805b9676c..baa0fd43d8 100644
--- a/packages/babel-core/src/config/files/index-browser.js
+++ b/packages/babel-core/src/config/files/index-browser.js
@@ -25,6 +25,13 @@ export function findRelativeConfig(
   return { pkg: null, config: null, ignore: null };
 }
 
+export function findRootConfig(
+  dirname: string,
+  envName: string, // eslint-disable-line no-unused-vars
+): ConfigFile | null {
+  return null;
+}
+
 export function loadConfig(
   name: string,
   dirname: string,
diff --git a/packages/babel-core/src/config/files/index.js b/packages/babel-core/src/config/files/index.js
index 06e8ce1fb2..9f8d9797bb 100644
--- a/packages/babel-core/src/config/files/index.js
+++ b/packages/babel-core/src/config/files/index.js
@@ -9,7 +9,11 @@ import typeof * as indexType from "./index";
 
 export { findPackageData } from "./package";
 
-export { findRelativeConfig, loadConfig } from "./configuration";
+export {
+  findRelativeConfig,
+  findRootConfig,
+  loadConfig,
+} from "./configuration";
 export type {
   ConfigFile,
   IgnoreFile,
diff --git a/packages/babel-core/src/config/partial.js b/packages/babel-core/src/config/partial.js
index 83d0d08086..e0fa76b81a 100644
--- a/packages/babel-core/src/config/partial.js
+++ b/packages/babel-core/src/config/partial.js
@@ -17,6 +17,7 @@ export default function loadPrivatePartialConfig(
   context: ConfigContext,
   ignore: IgnoreFile | void,
   babelrc: ConfigFile | void,
+  config: ConfigFile | void,
 } | null {
   if (
     inputOpts != null &&
@@ -64,6 +65,7 @@ export default function loadPrivatePartialConfig(
     context,
     ignore: configChain.ignore,
     babelrc: configChain.babelrc,
+    config: configChain.config,
   };
 }
 
@@ -71,7 +73,7 @@ export function loadPartialConfig(inputOpts: mixed): PartialConfig | null {
   const result = loadPrivatePartialConfig(inputOpts);
   if (!result) return null;
 
-  const { options, babelrc, ignore } = result;
+  const { options, babelrc, ignore, config } = result;
 
   (options.plugins || []).forEach(item => {
     if (item.value instanceof Plugin) {
@@ -86,6 +88,7 @@ export function loadPartialConfig(inputOpts: mixed): PartialConfig | null {
     options,
     babelrc ? babelrc.filepath : undefined,
     ignore ? ignore.filepath : undefined,
+    config ? config.filepath : undefined,
   );
 }
 
@@ -99,15 +102,18 @@ class PartialConfig {
   options: ValidatedOptions;
   babelrc: string | void;
   babelignore: string | void;
+  config: string | void;
 
   constructor(
     options: ValidatedOptions,
     babelrc: string | void,
     ignore: string | void,
+    config: string | void,
   ) {
     this.options = options;
     this.babelignore = ignore;
     this.babelrc = babelrc;
+    this.config = config;
 
     // Freeze since this is a public API and it should be extremely obvious that
     // reassigning properties on here does nothing.
diff --git a/packages/babel-core/src/config/validation/option-assertions.js b/packages/babel-core/src/config/validation/option-assertions.js
index 97b860f016..b59454e875 100644
--- a/packages/babel-core/src/config/validation/option-assertions.js
+++ b/packages/babel-core/src/config/validation/option-assertions.js
@@ -1,6 +1,7 @@
 // @flow
 
 import type {
+  ConfigFileSearch,
   IgnoreList,
   IgnoreItem,
   PluginList,
@@ -164,6 +165,24 @@ function checkValidTest(value: mixed): boolean {
   );
 }
 
+export function assertConfigFileSearch(
+  key: string,
+  value: mixed,
+): ConfigFileSearch | void {
+  if (
+    value !== undefined &&
+    typeof value !== "boolean" &&
+    typeof value !== "string"
+  ) {
+    throw new Error(
+      `.${key} must be a undefined, a boolean, a string, ` +
+        `got ${JSON.stringify(value)}`,
+    );
+  }
+
+  return value;
+}
+
 export function assertPluginList(key: string, value: mixed): PluginList | void {
   const arr = assertArray(key, value);
   if (arr) {
diff --git a/packages/babel-core/src/config/validation/options.js b/packages/babel-core/src/config/validation/options.js
index 290d326d5b..51fe8c9c0d 100644
--- a/packages/babel-core/src/config/validation/options.js
+++ b/packages/babel-core/src/config/validation/options.js
@@ -13,6 +13,7 @@ import {
   assertIgnoreList,
   assertPluginList,
   assertConfigApplicableTest,
+  assertConfigFileSearch,
   assertFunction,
   assertSourceMaps,
   assertCompact,
@@ -23,6 +24,11 @@ import {
 
 const ROOT_VALIDATORS: ValidatorSet = {
   cwd: (assertString: Validator<$PropertyType<ValidatedOptions, "cwd">>),
+  root: (assertString: Validator<$PropertyType<ValidatedOptions, "root">>),
+  configFile: (assertConfigFileSearch: Validator<
+    $PropertyType<ValidatedOptions, "configFile">,
+  >),
+
   filename: (assertString: Validator<
     $PropertyType<ValidatedOptions, "filename">,
   >),
@@ -152,6 +158,8 @@ export type ValidatedOptions = {
   filenameRelative?: string,
   babelrc?: boolean,
   code?: boolean,
+  configFile?: ConfigFileSearch,
+  root?: string,
   ast?: boolean,
   inputSourceMap?: RootInputSourceMapOption,
   envName?: string,
@@ -223,6 +231,7 @@ export type PluginList = $ReadOnlyArray<PluginItem>;
 export type OverridesList = Array<ValidatedOptions>;
 export type ConfigApplicableTest = IgnoreItem | Array<IgnoreItem>;
 
+export type ConfigFileSearch = string | boolean;
 export type SourceMapsOption = boolean | "inline" | "both";
 export type SourceTypeOption = "module" | "script" | "unambiguous";
 export type CompactOption = boolean | "auto";