diff --git a/src/compiler/emitter.ts b/src/compiler/emitter.ts
index 165f0da5cfd..7d0a29f9e26 100644
--- a/src/compiler/emitter.ts
+++ b/src/compiler/emitter.ts
@@ -5477,7 +5477,11 @@ var __param = (this && this.__param) || function (paramIndex, decorator) {
                 Debug.assert(!exportFunctionForFile);
                 // make sure that  name of 'exports' function does not conflict with existing identifiers
                 exportFunctionForFile = makeUniqueName("exports");
-                write("System.register([");
+                write("System.register(");
+                if (node.moduleName) {
+                    write(`"${node.moduleName}", `);
+                }
+                write("[")
                 for (let i = 0; i < externalImports.length; ++i) {
                     let text = getExternalModuleNameText(externalImports[i]);
                     if (i !== 0) {
@@ -5563,8 +5567,8 @@ var __param = (this && this.__param) || function (paramIndex, decorator) {
 
                 writeLine();
                 write("define(");
-                if (node.amdModuleName) {
-                    write("\"" + node.amdModuleName + "\", ");
+                if (node.moduleName) {
+                    write("\"" + node.moduleName + "\", ");
                 }
                 emitAMDDependencies(node, /*includeNonAmdDependencies*/ true);
                 write(") {");
diff --git a/src/compiler/parser.ts b/src/compiler/parser.ts
index 055fc1b6f74..07da065c1ae 100644
--- a/src/compiler/parser.ts
+++ b/src/compiler/parser.ts
@@ -4820,7 +4820,7 @@ module ts {
 
             sourceFile.referencedFiles = referencedFiles;
             sourceFile.amdDependencies = amdDependencies;
-            sourceFile.amdModuleName = amdModuleName;
+            sourceFile.moduleName = amdModuleName;
         }
 
         function setExternalModuleIndicator(sourceFile: SourceFile) {
diff --git a/src/compiler/types.ts b/src/compiler/types.ts
index 1db5e57d298..1a72e9fc94a 100644
--- a/src/compiler/types.ts
+++ b/src/compiler/types.ts
@@ -1001,7 +1001,7 @@ module ts {
         text: string;
 
         amdDependencies: {path: string; name: string}[];
-        amdModuleName: string;
+        moduleName: string;
         referencedFiles: FileReference[];
 
         hasNoDefaultLib: boolean;
diff --git a/src/services/services.ts b/src/services/services.ts
index 6a497c87307..ece411ae1ea 100644
--- a/src/services/services.ts
+++ b/src/services/services.ts
@@ -735,7 +735,7 @@ module ts {
         public endOfFileToken: Node;
 
         public amdDependencies: { name: string; path: string }[];
-        public amdModuleName: string;
+        public moduleName: string;
         public referencedFiles: FileReference[];
 
         public syntacticDiagnostics: Diagnostic[];
@@ -1766,7 +1766,7 @@ module ts {
      * - noLib = true
      * - noResolve = true
      */
-    export function transpile(input: string, compilerOptions?: CompilerOptions, fileName?: string, diagnostics?: Diagnostic[]): string {
+    export function transpile(input: string, compilerOptions?: CompilerOptions, fileName?: string, diagnostics?: Diagnostic[], moduleName?: string): string {
         let options = compilerOptions ? clone(compilerOptions) : getDefaultCompilerOptions();
 
         options.isolatedModules = true;
@@ -1785,6 +1785,9 @@ module ts {
         // Parse
         let inputFileName = fileName || "module.ts";
         let sourceFile = createSourceFile(inputFileName, input, options.target);
+        if (moduleName) {
+            sourceFile.moduleName = moduleName;
+        }
 
         // Store syntactic diagnostics
         if (diagnostics && sourceFile.parseDiagnostics) {
diff --git a/tests/baselines/reference/systemModule12.errors.txt b/tests/baselines/reference/systemModule12.errors.txt
new file mode 100644
index 00000000000..5c89e2e65d6
--- /dev/null
+++ b/tests/baselines/reference/systemModule12.errors.txt
@@ -0,0 +1,10 @@
+tests/cases/compiler/systemModule12.ts(3,15): error TS2307: Cannot find module 'file1'.
+
+
+==== tests/cases/compiler/systemModule12.ts (1 errors) ====
+    
+    ///<amd-module name='NamedModule'/>
+    import n from 'file1'
+                  ~~~~~~~
+!!! error TS2307: Cannot find module 'file1'.
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/systemModule12.js b/tests/baselines/reference/systemModule12.js
new file mode 100644
index 00000000000..0b5f5a3e850
--- /dev/null
+++ b/tests/baselines/reference/systemModule12.js
@@ -0,0 +1,14 @@
+//// [systemModule12.ts]
+
+///<amd-module name='NamedModule'/>
+import n from 'file1'
+
+
+//// [systemModule12.js]
+System.register("NamedModule", [], function(exports_1) {
+    return {
+        setters:[],
+        execute: function() {
+        }
+    }
+});
diff --git a/tests/cases/compiler/systemModule12.ts b/tests/cases/compiler/systemModule12.ts
new file mode 100644
index 00000000000..690fabc0a28
--- /dev/null
+++ b/tests/cases/compiler/systemModule12.ts
@@ -0,0 +1,5 @@
+// @module: system
+// @isolatedModules: true
+
+///<amd-module name='NamedModule'/>
+import n from 'file1'