diff --git a/src/babel/transformation/file/index.js b/src/babel/transformation/file/index.js
index aef1cc1ee0..a3ed081aad 100644
--- a/src/babel/transformation/file/index.js
+++ b/src/babel/transformation/file/index.js
@@ -16,6 +16,7 @@ import Logger from "./logger";
 import parse from "../../helpers/parse";
 import Scope from "../../traversal/scope";
 import slash from "slash";
+import clone from "lodash/lang/clone";
 import * as util from  "../../util";
 import path from "path";
 import each from "lodash/collection/each";
@@ -120,7 +121,9 @@ export default class File {
         throw new Error("Deprecated option " + key + ": " + option.deprecated);
       }
 
-      if (val == null) val = option.default || val;
+      if (val == null) {
+        val = clone(option.default);
+      }
 
       var optionParser = optionParsers[option.type];
       if (optionParser) val = optionParser(key, val);
diff --git a/src/babel/transformation/file/options.json b/src/babel/transformation/file/options.json
index 513cd11528..6de2a68857 100644
--- a/src/babel/transformation/file/options.json
+++ b/src/babel/transformation/file/options.json
@@ -15,8 +15,9 @@
     "hidden": true
   },
 
-  "pluginOptions": {
-    "hidden": true
+  "extra": {
+    "hidden": true,
+    "default": {}
   },
 
   "moduleId": {
diff --git a/test/core/api.js b/test/core/api.js
index b662cc1fe1..9662ca8cd0 100644
--- a/test/core/api.js
+++ b/test/core/api.js
@@ -1,3 +1,5 @@
+require("../../lib/babel/api/node");
+
 var buildExternalHelpers = require("../../lib/babel/tools/build-external-helpers");
 var transform            = require("../../lib/babel/transformation");
 var assert               = require("assert");
@@ -21,6 +23,15 @@ suite("api", function () {
     }, /Unknown helper foob/);
   });
 
+  test("extra options", function () {
+    var file1 = new File({ extra: { foo: "bar" } });
+    assert.equal(file1.opts.extra.foo, "bar");
+
+    var file2 = new File;
+    var file3 = new File;
+    assert.ok(file2.opts.extra !== file3.opts.extra);
+  });
+
   suite("buildExternalHelpers", function () {
     test("all", function () {
       var script = buildExternalHelpers();