diff --git a/src/babel/transformation/modules/amd.js b/src/babel/transformation/modules/amd.js
index 1eed9c457d..99a67b451d 100644
--- a/src/babel/transformation/modules/amd.js
+++ b/src/babel/transformation/modules/amd.js
@@ -6,8 +6,8 @@ import * as util from  "../../util";
 import * as t from "../../types";
 
 export default class AMDFormatter extends DefaultFormatter {
-  init() {
-    CommonFormatter.prototype._init.call(this, this.hasNonDefaultExports);
+  setup() {
+    CommonFormatter.prototype._setup.call(this, this.hasNonDefaultExports);
   }
 
   buildDependencyLiterals() {
diff --git a/src/babel/transformation/modules/common.js b/src/babel/transformation/modules/common.js
index 20215af7c5..c631268768 100644
--- a/src/babel/transformation/modules/common.js
+++ b/src/babel/transformation/modules/common.js
@@ -4,11 +4,11 @@ import * as util from  "../../util";
 import * as t from "../../types";
 
 export default class CommonJSFormatter extends DefaultFormatter {
-  init() {
-    this._init(this.hasLocalExports);
+  setup() {
+    this._setup(this.hasLocalExports);
   }
 
-  _init(conditional) {
+  _setup(conditional) {
     var file  = this.file;
     var scope = file.scope;
 
diff --git a/src/babel/transformation/transformers/internal/modules.js b/src/babel/transformation/transformers/internal/modules.js
index 7fa03c8ee0..cb741bdc39 100644
--- a/src/babel/transformation/transformers/internal/modules.js
+++ b/src/babel/transformation/transformers/internal/modules.js
@@ -85,18 +85,28 @@ export function ExportNamedDeclaration(node, parent, scope) {
   }
 }
 
-export function Program(node) {
-  var imports = [];
-  var rest = [];
+export var Program = {
+  enter(node) {
+    var imports = [];
+    var rest = [];
 
-  for (var i = 0; i < node.body.length; i++) {
-    var bodyNode = node.body[i];
-    if (t.isImportDeclaration(bodyNode)) {
-      imports.push(bodyNode);
-    } else {
-      rest.push(bodyNode);
+    for (var i = 0; i < node.body.length; i++) {
+      var bodyNode = node.body[i];
+      if (t.isImportDeclaration(bodyNode)) {
+        imports.push(bodyNode);
+      } else {
+        rest.push(bodyNode);
+      }
+    }
+
+    node.body = imports.concat(rest);
+  },
+
+  exit(node, parent, scope, file) {
+    if (!file.transformers["es6.modules"].canTransform()) return;
+
+    if (file.moduleFormatter.setup) {
+      file.moduleFormatter.setup();
     }
   }
-
-  node.body = imports.concat(rest);
-}
+};
diff --git a/test/core/fixtures/transformation/es6.modules-common/module-shadow/actual.js b/test/core/fixtures/transformation/es6.modules-common/module-shadow/actual.js
new file mode 100644
index 0000000000..8ee185c87d
--- /dev/null
+++ b/test/core/fixtures/transformation/es6.modules-common/module-shadow/actual.js
@@ -0,0 +1,3 @@
+export function module() {
+  
+}
diff --git a/test/core/fixtures/transformation/es6.modules-common/module-shadow/expected.js b/test/core/fixtures/transformation/es6.modules-common/module-shadow/expected.js
new file mode 100644
index 0000000000..f6a92cc04b
--- /dev/null
+++ b/test/core/fixtures/transformation/es6.modules-common/module-shadow/expected.js
@@ -0,0 +1,8 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.module = _module;
+
+function _module() {}