diff --git a/lib/rollup.js b/lib/rollup.js
index 0ca922e..e830d51 100644
--- a/lib/rollup.js
+++ b/lib/rollup.js
@@ -290,33 +290,16 @@ exports.rollupTree = function(loader, tree, entryPoints, traceOpts, compileOpts)
       // replace the entry point module itself with the inlined subgraph module
       var curInlined = inlineMap[entryPoint] || [];
 
-      // merge all external deps across all inlined modules
-      // when a duplicate dependency is hit, throw as we don't 
-      // have the ability to handle renaming without https://github.com/rollup/rollup/issues/424
-      var mergedDepMap = extend({}, entryPointLoad.depMap);
-      var mergedDeps = [].concat(entryPointLoad.deps.filter(function(dep) {
-        return externals.indexOf(entryPointLoad.depMap[dep]) != -1;
-      }));
-
-      curInlined.forEach(function(inlinedModule) {
-        var inlinedLoad = tree[inlinedModule];
-        
-        mergedDeps = mergedDeps.concat(inlinedLoad.deps.filter(function(dep) {
-          if (externals.indexOf(inlinedLoad.depMap[dep]) != -1) {
-            if (mergedDeps.indexOf(dep) == -1)
-              return true;
-
-            if (inlinedLoad.depMap[dep] != mergedDepMap[dep])
-              throw new Error('Duplicate dependency "' + dep + '" while using Rollup on "' + inlinedModule + '". Rename the dependency, or post to https://github.com/rollup/rollup/issues/424.');
-          }
-        }));
-
-        extend(mergedDepMap, inlinedLoad.depMap);
+      // the process of running rollup will itself normalize all dependencies
+      // the depMap then just becomes the identity map
+      var inlinedDepMap = {};
+      aliasedExternals.forEach(function(dep) {
+        inlinedDepMap[dep] = dep;
       });
 
       rolledUpTree[entryPoint] = extend(extend({}, entryPointLoad), {
-        deps: mergedDeps,
-        depMap: mergedDepMap,
+        deps: aliasedExternals,
+        depMap: inlinedDepMap,
         metadata: extend(extend({}, entryPointLoad.metadata), {
           originalSource: undefined,
           sourceMap: output.map
diff --git a/package.json b/package.json
index db4d301..ad197d8 100644
--- a/package.json
+++ b/package.json
@@ -11,7 +11,7 @@
     "es6-template-strings": "^2.0.0",
     "glob": "^7.0.3",
     "mkdirp": "^0.5.1",
-    "rollup": "^0.25.0",
+    "rollup": "^0.26.4",
     "source-map": "^0.5.3",
     "systemjs": "^0.19.28",
     "traceur": "0.0.105",