diff --git a/packages/babel-core/src/transformation/file/options/option-manager.js b/packages/babel-core/src/transformation/file/options/option-manager.js
index 069dad9d9a..707d6a43ed 100644
--- a/packages/babel-core/src/transformation/file/options/option-manager.js
+++ b/packages/babel-core/src/transformation/file/options/option-manager.js
@@ -324,14 +324,16 @@ export default class OptionManager {
     }
   }
 
-  init(opts: Object): Object {
+  init(opts: Object = {}): Object {
+    let filename = opts.filename;
+    
     // resolve all .babelrc files
     if (opts.babelrc !== false) {
-      this.findConfigs(opts.filename);
+      this.findConfigs(filename);
     }
 
     // merge in base options
-    this.mergeOptions(opts, "base");
+    this.mergeOptions(opts, "base", null, filename && path.dirname(filename));
 
     // normalise
     this.normaliseOptions(opts);
diff --git a/packages/babel-register/src/node.js b/packages/babel-register/src/node.js
index 4a6c757a90..2006e35212 100644
--- a/packages/babel-register/src/node.js
+++ b/packages/babel-register/src/node.js
@@ -46,14 +46,15 @@ function mtime(filename) {
   return +fs.statSync(filename).mtime;
 }
 
-function compile(filename, opts = {}) {
+function compile(filename) {
   let result;
 
-  opts.filename = filename;
-
   let optsManager = new OptionManager;
-  optsManager.mergeOptions(deepClone(transformOpts));
-  opts = optsManager.init(opts);
+
+  // merge in base options and resolve all the plugins and presets relative to this file
+  optsManager.mergeOptions(deepClone(transformOpts), "base", null, path.dirname(filename));
+
+  let opts = optsManager.init({ filename });
 
   let cacheKey = `${JSON.stringify(opts)}:${babel.version}`;