diff --git a/src/compiler/emitter.ts b/src/compiler/emitter.ts
index 11942562dcbe7..71187b2096092 100644
--- a/src/compiler/emitter.ts
+++ b/src/compiler/emitter.ts
@@ -446,7 +446,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
             /** If removeComments is true, no leading-comments needed to be emitted **/
             let emitLeadingCommentsOfPosition = compilerOptions.removeComments ? function (pos: number) { } : emitLeadingCommentsOfPositionWorker;
 
-            let moduleEmitDelegates: Map<(node: SourceFile, startIndex: number) => void> = {
+            let moduleEmitDelegates: Map<(node: SourceFile) => void> = {
                 [ModuleKind.ES6]: emitES6Module,
                 [ModuleKind.AMD]: emitAMDModule,
                 [ModuleKind.System]: emitSystemModule,
@@ -6594,7 +6594,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 write("}"); // execute
             }
 
-            function emitSystemModule(node: SourceFile, startIndex: number): void {
+            function emitSystemModule(node: SourceFile): void {
                 collectExternalModuleInfo(node);
                 // System modules has the following shape
                 // System.register(['dep-1', ... 'dep-n'], function(exports) {/* module body function */})
@@ -6639,6 +6639,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 write(`], function(${exportFunctionForFile}) {`);
                 writeLine();
                 increaseIndent();
+                let startIndex = emitDirectivePrologues(node.statements, /*startWithNewLine*/ true);
                 emitEmitHelpers(node);
                 emitCaptureThisForNodeIfNecessary(node);
                 emitSystemModuleBody(node, dependencyGroups, startIndex);
@@ -6732,7 +6733,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 write(") {");
             }
 
-            function emitAMDModule(node: SourceFile, startIndex: number) {
+            function emitAMDModule(node: SourceFile) {
                 emitEmitHelpers(node);
                 collectExternalModuleInfo(node);
 
@@ -6743,6 +6744,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 }
                 emitAMDDependencies(node, /*includeNonAmdDependencies*/ true);
                 increaseIndent();
+                let startIndex = emitDirectivePrologues(node.statements, /*startWithNewLine*/ true);
                 emitExportStarHelper();
                 emitCaptureThisForNodeIfNecessary(node);
                 emitLinesStartingAt(node.statements, startIndex);
@@ -6753,7 +6755,8 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 write("});");
             }
 
-            function emitCommonJSModule(node: SourceFile, startIndex: number) {
+            function emitCommonJSModule(node: SourceFile) {
+                let startIndex = emitDirectivePrologues(node.statements, /*startWithNewLine*/ false);
                 emitEmitHelpers(node);
                 collectExternalModuleInfo(node);
                 emitExportStarHelper();
@@ -6763,7 +6766,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 emitExportEquals(/*emitAsReturn*/ false);
             }
 
-            function emitUMDModule(node: SourceFile, startIndex: number) {
+            function emitUMDModule(node: SourceFile) {
                 emitEmitHelpers(node);
                 collectExternalModuleInfo(node);
 
@@ -6782,6 +6785,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
 })(`);
                 emitAMDFactoryHeader(dependencyNames);
                 increaseIndent();
+                let startIndex = emitDirectivePrologues(node.statements, /*startWithNewLine*/ true);
                 emitExportStarHelper();
                 emitCaptureThisForNodeIfNecessary(node);
                 emitLinesStartingAt(node.statements, startIndex);
@@ -6792,11 +6796,12 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 write("});");
             }
 
-            function emitES6Module(node: SourceFile, startIndex: number) {
+            function emitES6Module(node: SourceFile) {
                 externalImports = undefined;
                 exportSpecifiers = undefined;
                 exportEquals = undefined;
                 hasExportStars = false;
+                let startIndex = emitDirectivePrologues(node.statements, /*startWithNewLine*/ false);
                 emitEmitHelpers(node);
                 emitCaptureThisForNodeIfNecessary(node);
                 emitLinesStartingAt(node.statements, startIndex);
@@ -6985,14 +6990,13 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 emitShebang();
                 emitDetachedComments(node);
 
-                // emit prologue directives prior to __extends
-                let startIndex = emitDirectivePrologues(node.statements, /*startWithNewLine*/ false);
-
                 if (isExternalModule(node) || compilerOptions.isolatedModules) {
                     let emitModule = moduleEmitDelegates[modulekind] || moduleEmitDelegates[ModuleKind.CommonJS];
-                    emitModule(node, startIndex);
+                    emitModule(node);
                 }
                 else {
+                    // emit prologue directives prior to __extends
+                    let startIndex = emitDirectivePrologues(node.statements, /*startWithNewLine*/ false);
                     externalImports = undefined;
                     exportSpecifiers = undefined;
                     exportEquals = undefined;
diff --git a/tests/baselines/reference/modulePrologueAMD.js b/tests/baselines/reference/modulePrologueAMD.js
new file mode 100644
index 0000000000000..904808b9f6b6d
--- /dev/null
+++ b/tests/baselines/reference/modulePrologueAMD.js
@@ -0,0 +1,15 @@
+//// [modulePrologueAMD.ts]
+"use strict";
+
+export class Foo {}
+
+//// [modulePrologueAMD.js]
+define(["require", "exports"], function (require, exports) {
+    "use strict";
+    var Foo = (function () {
+        function Foo() {
+        }
+        return Foo;
+    })();
+    exports.Foo = Foo;
+});
diff --git a/tests/baselines/reference/modulePrologueAMD.symbols b/tests/baselines/reference/modulePrologueAMD.symbols
new file mode 100644
index 0000000000000..d6bb74d951ace
--- /dev/null
+++ b/tests/baselines/reference/modulePrologueAMD.symbols
@@ -0,0 +1,6 @@
+=== tests/cases/compiler/modulePrologueAMD.ts ===
+"use strict";
+
+export class Foo {}
+>Foo : Symbol(Foo, Decl(modulePrologueAMD.ts, 0, 13))
+
diff --git a/tests/baselines/reference/modulePrologueAMD.types b/tests/baselines/reference/modulePrologueAMD.types
new file mode 100644
index 0000000000000..b57b5a8bf2f33
--- /dev/null
+++ b/tests/baselines/reference/modulePrologueAMD.types
@@ -0,0 +1,7 @@
+=== tests/cases/compiler/modulePrologueAMD.ts ===
+"use strict";
+>"use strict" : string
+
+export class Foo {}
+>Foo : Foo
+
diff --git a/tests/baselines/reference/modulePrologueCommonjs.js b/tests/baselines/reference/modulePrologueCommonjs.js
new file mode 100644
index 0000000000000..67b704a365070
--- /dev/null
+++ b/tests/baselines/reference/modulePrologueCommonjs.js
@@ -0,0 +1,13 @@
+//// [modulePrologueCommonjs.ts]
+"use strict";
+
+export class Foo {}
+
+//// [modulePrologueCommonjs.js]
+"use strict";
+var Foo = (function () {
+    function Foo() {
+    }
+    return Foo;
+})();
+exports.Foo = Foo;
diff --git a/tests/baselines/reference/modulePrologueCommonjs.symbols b/tests/baselines/reference/modulePrologueCommonjs.symbols
new file mode 100644
index 0000000000000..01a2da349f2b2
--- /dev/null
+++ b/tests/baselines/reference/modulePrologueCommonjs.symbols
@@ -0,0 +1,6 @@
+=== tests/cases/compiler/modulePrologueCommonjs.ts ===
+"use strict";
+
+export class Foo {}
+>Foo : Symbol(Foo, Decl(modulePrologueCommonjs.ts, 0, 13))
+
diff --git a/tests/baselines/reference/modulePrologueCommonjs.types b/tests/baselines/reference/modulePrologueCommonjs.types
new file mode 100644
index 0000000000000..5d76532b3e47b
--- /dev/null
+++ b/tests/baselines/reference/modulePrologueCommonjs.types
@@ -0,0 +1,7 @@
+=== tests/cases/compiler/modulePrologueCommonjs.ts ===
+"use strict";
+>"use strict" : string
+
+export class Foo {}
+>Foo : Foo
+
diff --git a/tests/baselines/reference/modulePrologueES6.js b/tests/baselines/reference/modulePrologueES6.js
new file mode 100644
index 0000000000000..e34f85c9d8d36
--- /dev/null
+++ b/tests/baselines/reference/modulePrologueES6.js
@@ -0,0 +1,9 @@
+//// [modulePrologueES6.ts]
+"use strict";
+
+export class Foo {}
+
+//// [modulePrologueES6.js]
+"use strict";
+export class Foo {
+}
diff --git a/tests/baselines/reference/modulePrologueES6.symbols b/tests/baselines/reference/modulePrologueES6.symbols
new file mode 100644
index 0000000000000..f45180a6998b3
--- /dev/null
+++ b/tests/baselines/reference/modulePrologueES6.symbols
@@ -0,0 +1,6 @@
+=== tests/cases/compiler/modulePrologueES6.ts ===
+"use strict";
+
+export class Foo {}
+>Foo : Symbol(Foo, Decl(modulePrologueES6.ts, 0, 13))
+
diff --git a/tests/baselines/reference/modulePrologueES6.types b/tests/baselines/reference/modulePrologueES6.types
new file mode 100644
index 0000000000000..5f09a60ac6aa7
--- /dev/null
+++ b/tests/baselines/reference/modulePrologueES6.types
@@ -0,0 +1,7 @@
+=== tests/cases/compiler/modulePrologueES6.ts ===
+"use strict";
+>"use strict" : string
+
+export class Foo {}
+>Foo : Foo
+
diff --git a/tests/baselines/reference/modulePrologueSystem.js b/tests/baselines/reference/modulePrologueSystem.js
new file mode 100644
index 0000000000000..91703d1c7fba7
--- /dev/null
+++ b/tests/baselines/reference/modulePrologueSystem.js
@@ -0,0 +1,21 @@
+//// [modulePrologueSystem.ts]
+"use strict";
+
+export class Foo {}
+
+//// [modulePrologueSystem.js]
+System.register([], function(exports_1) {
+    "use strict";
+    var Foo;
+    return {
+        setters:[],
+        execute: function() {
+            Foo = (function () {
+                function Foo() {
+                }
+                return Foo;
+            })();
+            exports_1("Foo", Foo);
+        }
+    }
+});
diff --git a/tests/baselines/reference/modulePrologueSystem.symbols b/tests/baselines/reference/modulePrologueSystem.symbols
new file mode 100644
index 0000000000000..9e5ed9d452a2f
--- /dev/null
+++ b/tests/baselines/reference/modulePrologueSystem.symbols
@@ -0,0 +1,6 @@
+=== tests/cases/compiler/modulePrologueSystem.ts ===
+"use strict";
+
+export class Foo {}
+>Foo : Symbol(Foo, Decl(modulePrologueSystem.ts, 0, 13))
+
diff --git a/tests/baselines/reference/modulePrologueSystem.types b/tests/baselines/reference/modulePrologueSystem.types
new file mode 100644
index 0000000000000..ac0d52e4a2b8f
--- /dev/null
+++ b/tests/baselines/reference/modulePrologueSystem.types
@@ -0,0 +1,7 @@
+=== tests/cases/compiler/modulePrologueSystem.ts ===
+"use strict";
+>"use strict" : string
+
+export class Foo {}
+>Foo : Foo
+
diff --git a/tests/baselines/reference/modulePrologueUmd.js b/tests/baselines/reference/modulePrologueUmd.js
new file mode 100644
index 0000000000000..65803af6cadec
--- /dev/null
+++ b/tests/baselines/reference/modulePrologueUmd.js
@@ -0,0 +1,22 @@
+//// [modulePrologueUmd.ts]
+"use strict";
+
+export class Foo {}
+
+//// [modulePrologueUmd.js]
+(function (factory) {
+    if (typeof module === 'object' && typeof module.exports === 'object') {
+        var v = factory(require, exports); if (v !== undefined) module.exports = v;
+    }
+    else if (typeof define === 'function' && define.amd) {
+        define(["require", "exports"], factory);
+    }
+})(function (require, exports) {
+    "use strict";
+    var Foo = (function () {
+        function Foo() {
+        }
+        return Foo;
+    })();
+    exports.Foo = Foo;
+});
diff --git a/tests/baselines/reference/modulePrologueUmd.symbols b/tests/baselines/reference/modulePrologueUmd.symbols
new file mode 100644
index 0000000000000..3b015b2ea448e
--- /dev/null
+++ b/tests/baselines/reference/modulePrologueUmd.symbols
@@ -0,0 +1,6 @@
+=== tests/cases/compiler/modulePrologueUmd.ts ===
+"use strict";
+
+export class Foo {}
+>Foo : Symbol(Foo, Decl(modulePrologueUmd.ts, 0, 13))
+
diff --git a/tests/baselines/reference/modulePrologueUmd.types b/tests/baselines/reference/modulePrologueUmd.types
new file mode 100644
index 0000000000000..2a1064da8e2a3
--- /dev/null
+++ b/tests/baselines/reference/modulePrologueUmd.types
@@ -0,0 +1,7 @@
+=== tests/cases/compiler/modulePrologueUmd.ts ===
+"use strict";
+>"use strict" : string
+
+export class Foo {}
+>Foo : Foo
+
diff --git a/tests/cases/compiler/modulePrologueAMD.ts b/tests/cases/compiler/modulePrologueAMD.ts
new file mode 100644
index 0000000000000..d5473798ee021
--- /dev/null
+++ b/tests/cases/compiler/modulePrologueAMD.ts
@@ -0,0 +1,4 @@
+// @module: amd
+"use strict";
+
+export class Foo {}
\ No newline at end of file
diff --git a/tests/cases/compiler/modulePrologueCommonjs.ts b/tests/cases/compiler/modulePrologueCommonjs.ts
new file mode 100644
index 0000000000000..d6ef5e820a381
--- /dev/null
+++ b/tests/cases/compiler/modulePrologueCommonjs.ts
@@ -0,0 +1,4 @@
+// @module: commonjs
+"use strict";
+
+export class Foo {}
\ No newline at end of file
diff --git a/tests/cases/compiler/modulePrologueES6.ts b/tests/cases/compiler/modulePrologueES6.ts
new file mode 100644
index 0000000000000..a0782891cbab7
--- /dev/null
+++ b/tests/cases/compiler/modulePrologueES6.ts
@@ -0,0 +1,5 @@
+// @module: es6
+// @target: es6
+"use strict";
+
+export class Foo {}
\ No newline at end of file
diff --git a/tests/cases/compiler/modulePrologueSystem.ts b/tests/cases/compiler/modulePrologueSystem.ts
new file mode 100644
index 0000000000000..d336bdb8950a5
--- /dev/null
+++ b/tests/cases/compiler/modulePrologueSystem.ts
@@ -0,0 +1,4 @@
+// @module: system
+"use strict";
+
+export class Foo {}
\ No newline at end of file
diff --git a/tests/cases/compiler/modulePrologueUmd.ts b/tests/cases/compiler/modulePrologueUmd.ts
new file mode 100644
index 0000000000000..2660ca75081fe
--- /dev/null
+++ b/tests/cases/compiler/modulePrologueUmd.ts
@@ -0,0 +1,4 @@
+// @module: umd
+"use strict";
+
+export class Foo {}
\ No newline at end of file