diff --git a/src/babel/api/register/node.js b/src/babel/api/register/node.js
index 86bee9a300..6a021cb328 100644
--- a/src/babel/api/register/node.js
+++ b/src/babel/api/register/node.js
@@ -6,6 +6,7 @@ import * as babel from "../node";
 import each from "lodash/collection/each";
 import * as util from  "../../util";
 import fs from "fs";
+import path from "path";
 
 sourceMapSupport.install({
   handleUncaughtExceptions: false,
@@ -37,6 +38,12 @@ var only;
 var oldHandlers   = {};
 var maps          = {};
 
+var cwd = require.main ? require.main.filename : process.cwd();
+
+var getRelativePath = function (filename){
+  return path.relative(cwd, filename);
+};
+
 var mtime = function (filename) {
   return +fs.statSync(filename).mtime;
 };
@@ -81,7 +88,7 @@ var compile = function (filename) {
 
 var shouldIgnore = function (filename) {
   if (!ignore && !only) {
-    return /node_modules/.test(filename);
+    return /node_modules/.test(getRelativePath(filename));
   } else {
     return util.shouldIgnore(filename, ignore || [], only || []);
   }