diff --git a/src/compiler/emitter.ts b/src/compiler/emitter.ts
index 98c551027ff..bef04e50302 100644
--- a/src/compiler/emitter.ts
+++ b/src/compiler/emitter.ts
@@ -6259,6 +6259,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 write(`], function(${exportFunctionForFile}) {`);
                 writeLine();
                 increaseIndent();
+                emitEmitHelpers(node);
                 emitCaptureThisForNodeIfNecessary(node);
                 emitSystemModuleBody(node, startIndex);
                 decreaseIndent();
@@ -6330,6 +6331,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
             }
 
             function emitAMDModule(node: SourceFile, startIndex: number) {
+                emitEmitHelpers(node);
                 collectExternalModuleInfo(node);
 
                 writeLine();
@@ -6351,6 +6353,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
             }
 
             function emitCommonJSModule(node: SourceFile, startIndex: number) {
+                emitEmitHelpers(node);
                 collectExternalModuleInfo(node);
                 emitExportStarHelper();
                 emitCaptureThisForNodeIfNecessary(node);
@@ -6360,6 +6363,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
             }
 
             function emitUMDModule(node: SourceFile, startIndex: number) {
+                emitEmitHelpers(node);
                 collectExternalModuleInfo(node);
 
                 // Module is detected first to support Browserify users that load into a browser with an AMD loader
@@ -6389,6 +6393,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 exportSpecifiers = undefined;
                 exportEquals = undefined;
                 hasExportStars = false;
+                emitEmitHelpers(node);
                 emitCaptureThisForNodeIfNecessary(node);
                 emitLinesStartingAt(node.statements, startIndex);
                 emitTempDeclarations(/*newLine*/ true);
@@ -6527,14 +6532,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 }
             }
 
-            function emitSourceFileNode(node: SourceFile) {
-                // Start new file on new line
-                writeLine();
-                emitDetachedComments(node);
-
-                // emit prologue directives prior to __extends
-                let startIndex = emitDirectivePrologues(node.statements, /*startWithNewLine*/ false);
-
+            function emitEmitHelpers(node: SourceFile): void {
                 // Only emit helpers if the user did not say otherwise.
                 if (!compilerOptions.noEmitHelpers) {
                     // Only Emit __extends function when target ES5.
@@ -6562,6 +6560,15 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                         awaiterEmitted = true;
                     }
                 }
+            }
+
+            function emitSourceFileNode(node: SourceFile) {
+                // Start new file on new line
+                writeLine();
+                emitDetachedComments(node);
+
+                // emit prologue directives prior to __extends
+                let startIndex = emitDirectivePrologues(node.statements, /*startWithNewLine*/ false);
 
                 if (isExternalModule(node) || compilerOptions.isolatedModules) {
                     if (languageVersion >= ScriptTarget.ES6) {
@@ -6585,6 +6592,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                     exportSpecifiers = undefined;
                     exportEquals = undefined;
                     hasExportStars = false;
+                    emitEmitHelpers(node);
                     emitCaptureThisForNodeIfNecessary(node);
                     emitLinesStartingAt(node.statements, startIndex);
                     emitTempDeclarations(/*newLine*/ true);
diff --git a/tests/baselines/reference/systemModuleWithSuperClass.js b/tests/baselines/reference/systemModuleWithSuperClass.js
new file mode 100644
index 00000000000..3484606ee0e
--- /dev/null
+++ b/tests/baselines/reference/systemModuleWithSuperClass.js
@@ -0,0 +1,55 @@
+//// [tests/cases/compiler/systemModuleWithSuperClass.ts] ////
+
+//// [foo.ts]
+
+export class Foo {
+    a: string;
+}
+
+//// [bar.ts]
+import {Foo} from './foo';
+export class Bar extends Foo {
+    b: string;
+}
+
+//// [foo.js]
+System.register([], function(exports_1) {
+    var Foo;
+    return {
+        setters:[],
+        execute: function() {
+            Foo = (function () {
+                function Foo() {
+                }
+                return Foo;
+            })();
+            exports_1("Foo", Foo);
+        }
+    }
+});
+//// [bar.js]
+System.register(['./foo'], function(exports_1) {
+    var __extends = (this && this.__extends) || function (d, b) {
+        for (var p in b) if (b.hasOwnProperty(p)) d[p] = b[p];
+        function __() { this.constructor = d; }
+        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+    };
+    var foo_1;
+    var Bar;
+    return {
+        setters:[
+            function (_foo_1) {
+                foo_1 = _foo_1;
+            }],
+        execute: function() {
+            Bar = (function (_super) {
+                __extends(Bar, _super);
+                function Bar() {
+                    _super.apply(this, arguments);
+                }
+                return Bar;
+            })(foo_1.Foo);
+            exports_1("Bar", Bar);
+        }
+    }
+});
diff --git a/tests/baselines/reference/systemModuleWithSuperClass.symbols b/tests/baselines/reference/systemModuleWithSuperClass.symbols
new file mode 100644
index 00000000000..46354333479
--- /dev/null
+++ b/tests/baselines/reference/systemModuleWithSuperClass.symbols
@@ -0,0 +1,20 @@
+=== tests/cases/compiler/foo.ts ===
+
+export class Foo {
+>Foo : Symbol(Foo, Decl(foo.ts, 0, 0))
+
+    a: string;
+>a : Symbol(a, Decl(foo.ts, 1, 18))
+}
+
+=== tests/cases/compiler/bar.ts ===
+import {Foo} from './foo';
+>Foo : Symbol(Foo, Decl(bar.ts, 0, 8))
+
+export class Bar extends Foo {
+>Bar : Symbol(Bar, Decl(bar.ts, 0, 26))
+>Foo : Symbol(Foo, Decl(bar.ts, 0, 8))
+
+    b: string;
+>b : Symbol(b, Decl(bar.ts, 1, 30))
+}
diff --git a/tests/baselines/reference/systemModuleWithSuperClass.types b/tests/baselines/reference/systemModuleWithSuperClass.types
new file mode 100644
index 00000000000..130f53f0ce3
--- /dev/null
+++ b/tests/baselines/reference/systemModuleWithSuperClass.types
@@ -0,0 +1,20 @@
+=== tests/cases/compiler/foo.ts ===
+
+export class Foo {
+>Foo : Foo
+
+    a: string;
+>a : string
+}
+
+=== tests/cases/compiler/bar.ts ===
+import {Foo} from './foo';
+>Foo : typeof Foo
+
+export class Bar extends Foo {
+>Bar : Bar
+>Foo : Foo
+
+    b: string;
+>b : string
+}
diff --git a/tests/cases/compiler/systemModuleWithSuperClass.ts b/tests/cases/compiler/systemModuleWithSuperClass.ts
new file mode 100644
index 00000000000..2f1c21f4d48
--- /dev/null
+++ b/tests/cases/compiler/systemModuleWithSuperClass.ts
@@ -0,0 +1,12 @@
+// @module: system
+
+// @Filename: foo.ts
+export class Foo {
+    a: string;
+}
+
+// @Filename: bar.ts
+import {Foo} from './foo';
+export class Bar extends Foo {
+    b: string;
+}
\ No newline at end of file