diff --git a/test/comparison-tests/node_modules-subdir/app.ts b/test/comparison-tests/node_modules-subdir/app.ts
new file mode 100644
index 000000000..efd8ba5a8
--- /dev/null
+++ b/test/comparison-tests/node_modules-subdir/app.ts
@@ -0,0 +1,2 @@
+import * as bar from "foo/bar"
+console.log(bar)
\ No newline at end of file
diff --git a/test/comparison-tests/node_modules-subdir/expectedOutput-2.0/bundle.js b/test/comparison-tests/node_modules-subdir/expectedOutput-2.0/bundle.js
new file mode 100644
index 000000000..82fa821e0
--- /dev/null
+++ b/test/comparison-tests/node_modules-subdir/expectedOutput-2.0/bundle.js
@@ -0,0 +1,53 @@
+/******/ (function(modules) { // webpackBootstrap
+/******/ 	// The module cache
+/******/ 	var installedModules = {};
+
+/******/ 	// The require function
+/******/ 	function __webpack_require__(moduleId) {
+
+/******/ 		// Check if module is in cache
+/******/ 		if(installedModules[moduleId])
+/******/ 			return installedModules[moduleId].exports;
+
+/******/ 		// Create a new module (and put it into the cache)
+/******/ 		var module = installedModules[moduleId] = {
+/******/ 			exports: {},
+/******/ 			id: moduleId,
+/******/ 			loaded: false
+/******/ 		};
+
+/******/ 		// Execute the module function
+/******/ 		modules[moduleId].call(module.exports, module, module.exports, __webpack_require__);
+
+/******/ 		// Flag the module as loaded
+/******/ 		module.loaded = true;
+
+/******/ 		// Return the exports of the module
+/******/ 		return module.exports;
+/******/ 	}
+
+
+/******/ 	// expose the modules object (__webpack_modules__)
+/******/ 	__webpack_require__.m = modules;
+
+/******/ 	// expose the module cache
+/******/ 	__webpack_require__.c = installedModules;
+
+/******/ 	// __webpack_public_path__
+/******/ 	__webpack_require__.p = "";
+
+/******/ 	// Load entry module and return exports
+/******/ 	return __webpack_require__(0);
+/******/ })
+/************************************************************************/
+/******/ ([
+/* 0 */
+/***/ function(module, exports, __webpack_require__) {
+
+	"use strict";
+	var bar = __webpack_require__(!(function webpackMissingModule() { var e = new Error("Cannot find module \"foo/bar\""); e.code = 'MODULE_NOT_FOUND'; throw e; }()));
+	console.log(bar);
+
+
+/***/ }
+/******/ ]);
\ No newline at end of file
diff --git a/test/comparison-tests/node_modules-subdir/expectedOutput-2.0/bundle.transpiled.js b/test/comparison-tests/node_modules-subdir/expectedOutput-2.0/bundle.transpiled.js
new file mode 100644
index 000000000..fe782200b
--- /dev/null
+++ b/test/comparison-tests/node_modules-subdir/expectedOutput-2.0/bundle.transpiled.js
@@ -0,0 +1,61 @@
+/******/ (function(modules) { // webpackBootstrap
+/******/ 	// The module cache
+/******/ 	var installedModules = {};
+
+/******/ 	// The require function
+/******/ 	function __webpack_require__(moduleId) {
+
+/******/ 		// Check if module is in cache
+/******/ 		if(installedModules[moduleId])
+/******/ 			return installedModules[moduleId].exports;
+
+/******/ 		// Create a new module (and put it into the cache)
+/******/ 		var module = installedModules[moduleId] = {
+/******/ 			exports: {},
+/******/ 			id: moduleId,
+/******/ 			loaded: false
+/******/ 		};
+
+/******/ 		// Execute the module function
+/******/ 		modules[moduleId].call(module.exports, module, module.exports, __webpack_require__);
+
+/******/ 		// Flag the module as loaded
+/******/ 		module.loaded = true;
+
+/******/ 		// Return the exports of the module
+/******/ 		return module.exports;
+/******/ 	}
+
+
+/******/ 	// expose the modules object (__webpack_modules__)
+/******/ 	__webpack_require__.m = modules;
+
+/******/ 	// expose the module cache
+/******/ 	__webpack_require__.c = installedModules;
+
+/******/ 	// __webpack_public_path__
+/******/ 	__webpack_require__.p = "";
+
+/******/ 	// Load entry module and return exports
+/******/ 	return __webpack_require__(0);
+/******/ })
+/************************************************************************/
+/******/ ([
+/* 0 */
+/***/ function(module, exports, __webpack_require__) {
+
+	"use strict";
+	var bar = __webpack_require__(1);
+	console.log(bar);
+
+
+/***/ },
+/* 1 */
+/***/ function(module, exports) {
+
+	"use strict";
+	exports.bar = "sample";
+
+
+/***/ }
+/******/ ]);
\ No newline at end of file
diff --git a/test/comparison-tests/node_modules-subdir/expectedOutput-2.0/output.transpiled.txt b/test/comparison-tests/node_modules-subdir/expectedOutput-2.0/output.transpiled.txt
new file mode 100644
index 000000000..e1150ce03
--- /dev/null
+++ b/test/comparison-tests/node_modules-subdir/expectedOutput-2.0/output.transpiled.txt
@@ -0,0 +1,5 @@
+    Asset     Size  Chunks             Chunk Names
+bundle.js  1.57 kB       0  [emitted]  main
+chunk    {0} bundle.js (main) 100 bytes [rendered]
+    [0] ./.test/node_modules-subdir/app.ts 62 bytes {0} [built]
+    [1] ./.test/node_modules-subdir/~/foo/bar/index.ts 38 bytes {0} [built]
\ No newline at end of file
diff --git a/test/comparison-tests/node_modules-subdir/expectedOutput-2.0/output.txt b/test/comparison-tests/node_modules-subdir/expectedOutput-2.0/output.txt
new file mode 100644
index 000000000..a7b67e94e
--- /dev/null
+++ b/test/comparison-tests/node_modules-subdir/expectedOutput-2.0/output.txt
@@ -0,0 +1,9 @@
+    Asset     Size  Chunks             Chunk Names
+bundle.js  1.61 kB       0  [emitted]  main
+chunk    {0} bundle.js (main) 62 bytes [rendered]
+    [0] ./.test/node_modules-subdir/app.ts 62 bytes {0} [built] [1 error]
+
+ERROR in ./.test/node_modules-subdir/~/foo/bar/index.ts
+Module build failed: Error: Typescript emitted no output for node_modules/foo/bar/index.ts
+    at Object.loader (dist/index.js:27:15)
+ @ ./.test/node_modules-subdir/app.ts 2:10-28
\ No newline at end of file
diff --git a/test/comparison-tests/node_modules-subdir/node_modules/foo/bar/index.ts b/test/comparison-tests/node_modules-subdir/node_modules/foo/bar/index.ts
new file mode 100644
index 000000000..6ba93a568
--- /dev/null
+++ b/test/comparison-tests/node_modules-subdir/node_modules/foo/bar/index.ts
@@ -0,0 +1 @@
+export const bar = "sample"
diff --git a/test/comparison-tests/node_modules-subdir/node_modules/foo/package.json b/test/comparison-tests/node_modules-subdir/node_modules/foo/package.json
new file mode 100644
index 000000000..5326b76a5
--- /dev/null
+++ b/test/comparison-tests/node_modules-subdir/node_modules/foo/package.json
@@ -0,0 +1,12 @@
+{
+  "name": "foo",
+  "version": "1.0.0",
+  "description": "",
+  "main": "index.js",
+  "scripts": {
+    "test": "echo \"Error: no test specified\" && exit 1"
+  },
+  "keywords": [],
+  "author": "",
+  "license": "ISC"
+}
diff --git a/test/comparison-tests/node_modules-subdir/tsconfig.json b/test/comparison-tests/node_modules-subdir/tsconfig.json
new file mode 100644
index 000000000..c99e8cde6
--- /dev/null
+++ b/test/comparison-tests/node_modules-subdir/tsconfig.json
@@ -0,0 +1,5 @@
+{
+    "compilerOptions": {
+        "target": "es5"
+    }
+}
\ No newline at end of file
diff --git a/test/comparison-tests/node_modules-subdir/webpack.config.js b/test/comparison-tests/node_modules-subdir/webpack.config.js
new file mode 100644
index 000000000..aae026d84
--- /dev/null
+++ b/test/comparison-tests/node_modules-subdir/webpack.config.js
@@ -0,0 +1,17 @@
+module.exports = {
+    entry: './app.ts',
+    output: {
+        filename: 'bundle.js'
+    },
+    resolve: {
+        extensions: ['', '.ts', '.js']
+    },
+    module: {
+        loaders: [
+            { test: /\.ts$/, loader: 'ts-loader' }
+        ]
+    }
+}
+
+// for test harness purposes only, you would not need this in a normal project
+module.exports.resolveLoader = { alias: { 'ts-loader': require('path').join(__dirname, "../../index.js") } }
\ No newline at end of file