diff --git a/src/compiler/program.ts b/src/compiler/program.ts
index 1ef5d6bfba1..bf5b7cb5727 100644
--- a/src/compiler/program.ts
+++ b/src/compiler/program.ts
@@ -2076,7 +2076,10 @@ namespace ts {
             }
 
             // Cannot specify module gen that isn't amd or system with --out
-            if (outFile && options.module && !(options.module === ModuleKind.AMD || options.module === ModuleKind.System)) {
+            // Report this error if user specified --module moduleKind 
+            // or if there is external module in compilation which defaults to commonjs
+            const emitModuleKind = getEmitModuleKind(options);
+            if (outFile && (options.module || firstExternalModuleSourceFile) && !(emitModuleKind === ModuleKind.AMD || emitModuleKind === ModuleKind.System)) {
                 programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Only_amd_and_system_modules_are_supported_alongside_0, options.out ? "out" : "outFile"));
             }
 
diff --git a/tests/baselines/reference/isolatedModulesOut.errors.txt b/tests/baselines/reference/isolatedModulesOut.errors.txt
index 7d16ac94666..7df16139bfe 100644
--- a/tests/baselines/reference/isolatedModulesOut.errors.txt
+++ b/tests/baselines/reference/isolatedModulesOut.errors.txt
@@ -1,8 +1,10 @@
 error TS5053: Option 'out' cannot be specified with option 'isolatedModules'.
+error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
 tests/cases/compiler/file2.ts(1,1): error TS1208: Cannot compile namespaces when the '--isolatedModules' flag is provided.
 
 
 !!! error TS5053: Option 'out' cannot be specified with option 'isolatedModules'.
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
 ==== tests/cases/compiler/file1.ts (0 errors) ====
     
     export var x;
diff --git a/tests/baselines/reference/typeReferenceDirectives11.errors.txt b/tests/baselines/reference/typeReferenceDirectives11.errors.txt
new file mode 100644
index 00000000000..2acecc8de4c
--- /dev/null
+++ b/tests/baselines/reference/typeReferenceDirectives11.errors.txt
@@ -0,0 +1,17 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+==== /mod2.ts (0 errors) ====
+    
+    import {foo} from "./mod1";
+    export const bar = foo();
+==== /types/lib/index.d.ts (0 errors) ====
+    
+    
+    interface Lib { x }
+    
+==== /mod1.ts (0 errors) ====
+    
+    export function foo(): Lib { return {x: 1} }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/typeReferenceDirectives11.js b/tests/baselines/reference/typeReferenceDirectives11.js
deleted file mode 100644
index cb41c843adc..00000000000
--- a/tests/baselines/reference/typeReferenceDirectives11.js
+++ /dev/null
@@ -1,27 +0,0 @@
-//// [tests/cases/compiler/typeReferenceDirectives11.ts] ////
-
-//// [index.d.ts]
-
-
-interface Lib { x }
-
-//// [mod1.ts]
-
-export function foo(): Lib { return {x: 1} }
-
-//// [mod2.ts]
-
-import {foo} from "./mod1";
-export const bar = foo();
-
-//// [output.js]
-
-
-//// [output.d.ts]
-/// <reference types="lib" />
-declare module "mod1" {
-    export function foo(): Lib;
-}
-declare module "mod2" {
-    export const bar: Lib;
-}
diff --git a/tests/baselines/reference/typeReferenceDirectives11.symbols b/tests/baselines/reference/typeReferenceDirectives11.symbols
deleted file mode 100644
index 875bb2a0900..00000000000
--- a/tests/baselines/reference/typeReferenceDirectives11.symbols
+++ /dev/null
@@ -1,23 +0,0 @@
-=== /mod2.ts ===
-
-import {foo} from "./mod1";
->foo : Symbol(foo, Decl(mod2.ts, 1, 8))
-
-export const bar = foo();
->bar : Symbol(bar, Decl(mod2.ts, 2, 12))
->foo : Symbol(foo, Decl(mod2.ts, 1, 8))
-
-=== /types/lib/index.d.ts ===
-
-
-interface Lib { x }
->Lib : Symbol(Lib, Decl(index.d.ts, 0, 0))
->x : Symbol(Lib.x, Decl(index.d.ts, 2, 15))
-
-=== /mod1.ts ===
-
-export function foo(): Lib { return {x: 1} }
->foo : Symbol(foo, Decl(mod1.ts, 0, 0))
->Lib : Symbol(Lib, Decl(index.d.ts, 0, 0))
->x : Symbol(x, Decl(mod1.ts, 1, 37))
-
diff --git a/tests/baselines/reference/typeReferenceDirectives11.types b/tests/baselines/reference/typeReferenceDirectives11.types
deleted file mode 100644
index 93d80b7988a..00000000000
--- a/tests/baselines/reference/typeReferenceDirectives11.types
+++ /dev/null
@@ -1,26 +0,0 @@
-=== /mod2.ts ===
-
-import {foo} from "./mod1";
->foo : () => Lib
-
-export const bar = foo();
->bar : Lib
->foo() : Lib
->foo : () => Lib
-
-=== /types/lib/index.d.ts ===
-
-
-interface Lib { x }
->Lib : Lib
->x : any
-
-=== /mod1.ts ===
-
-export function foo(): Lib { return {x: 1} }
->foo : () => Lib
->Lib : Lib
->{x: 1} : { x: number; }
->x : number
->1 : number
-
diff --git a/tests/baselines/reference/typeReferenceDirectives12.errors.txt b/tests/baselines/reference/typeReferenceDirectives12.errors.txt
new file mode 100644
index 00000000000..1a1668ecfcd
--- /dev/null
+++ b/tests/baselines/reference/typeReferenceDirectives12.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+==== /mod2.ts (0 errors) ====
+    import { Cls } from "./main";
+    import "./mod1";
+    
+    export const cls = Cls;
+    export const foo = new Cls().foo();
+    export const bar = Cls.bar();
+==== /types/lib/index.d.ts (0 errors) ====
+    
+    
+    interface Lib { x }
+    
+==== /main.ts (0 errors) ====
+    export class Cls {
+        x
+    }
+    
+==== /mod1.ts (0 errors) ====
+    /// <reference types="lib" />
+    
+    import {Cls} from "./main";
+    Cls.prototype.foo = function() { return undefined; }
+    
+    declare module "./main" {
+        interface Cls {
+            foo(): Lib;
+        }
+        namespace Cls {
+            function bar(): Lib;
+        }
+    }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/typeReferenceDirectives12.js b/tests/baselines/reference/typeReferenceDirectives12.js
deleted file mode 100644
index c9c4a912da1..00000000000
--- a/tests/baselines/reference/typeReferenceDirectives12.js
+++ /dev/null
@@ -1,63 +0,0 @@
-//// [tests/cases/compiler/typeReferenceDirectives12.ts] ////
-
-//// [index.d.ts]
-
-
-interface Lib { x }
-
-//// [main.ts]
-export class Cls {
-    x
-}
-
-//// [mod1.ts]
-/// <reference types="lib" />
-
-import {Cls} from "./main";
-Cls.prototype.foo = function() { return undefined; }
-
-declare module "./main" {
-    interface Cls {
-        foo(): Lib;
-    }
-    namespace Cls {
-        function bar(): Lib;
-    }
-}
-
-//// [mod2.ts]
-import { Cls } from "./main";
-import "./mod1";
-
-export const cls = Cls;
-export const foo = new Cls().foo();
-export const bar = Cls.bar();
-
-//// [output.js]
-/// <reference types="lib" />
-
-
-//// [output.d.ts]
-/// <reference types="lib" />
-declare module "main" {
-    export class Cls {
-        x: any;
-    }
-}
-declare module "mod1" {
-    module "main" {
-        interface Cls {
-            foo(): Lib;
-        }
-        namespace Cls {
-            function bar(): Lib;
-        }
-    }
-}
-declare module "mod2" {
-    import { Cls } from "main";
-    import "mod1";
-    export const cls: typeof Cls;
-    export const foo: Lib;
-    export const bar: Lib;
-}
diff --git a/tests/baselines/reference/typeReferenceDirectives12.symbols b/tests/baselines/reference/typeReferenceDirectives12.symbols
deleted file mode 100644
index 30b24c39284..00000000000
--- a/tests/baselines/reference/typeReferenceDirectives12.symbols
+++ /dev/null
@@ -1,68 +0,0 @@
-=== /mod2.ts ===
-import { Cls } from "./main";
->Cls : Symbol(Cls, Decl(mod2.ts, 0, 8))
-
-import "./mod1";
-
-export const cls = Cls;
->cls : Symbol(cls, Decl(mod2.ts, 3, 12))
->Cls : Symbol(Cls, Decl(mod2.ts, 0, 8))
-
-export const foo = new Cls().foo();
->foo : Symbol(foo, Decl(mod2.ts, 4, 12))
->new Cls().foo : Symbol(Cls.foo, Decl(mod1.ts, 6, 19))
->Cls : Symbol(Cls, Decl(mod2.ts, 0, 8))
->foo : Symbol(Cls.foo, Decl(mod1.ts, 6, 19))
-
-export const bar = Cls.bar();
->bar : Symbol(bar, Decl(mod2.ts, 5, 12))
->Cls.bar : Symbol(Cls.bar, Decl(mod1.ts, 9, 19))
->Cls : Symbol(Cls, Decl(mod2.ts, 0, 8))
->bar : Symbol(Cls.bar, Decl(mod1.ts, 9, 19))
-
-=== /types/lib/index.d.ts ===
-
-
-interface Lib { x }
->Lib : Symbol(Lib, Decl(index.d.ts, 0, 0))
->x : Symbol(Lib.x, Decl(index.d.ts, 2, 15))
-
-=== /main.ts ===
-export class Cls {
->Cls : Symbol(Cls, Decl(main.ts, 0, 0), Decl(mod1.ts, 5, 25), Decl(mod1.ts, 8, 5))
-
-    x
->x : Symbol(Cls.x, Decl(main.ts, 0, 18))
-}
-
-=== /mod1.ts ===
-/// <reference types="lib" />
-
-import {Cls} from "./main";
->Cls : Symbol(Cls, Decl(mod1.ts, 2, 8))
-
-Cls.prototype.foo = function() { return undefined; }
->Cls.prototype.foo : Symbol(Cls.foo, Decl(mod1.ts, 6, 19))
->Cls.prototype : Symbol(Cls.prototype)
->Cls : Symbol(Cls, Decl(mod1.ts, 2, 8))
->prototype : Symbol(Cls.prototype)
->foo : Symbol(Cls.foo, Decl(mod1.ts, 6, 19))
->undefined : Symbol(undefined)
-
-declare module "./main" {
-    interface Cls {
->Cls : Symbol(Cls, Decl(main.ts, 0, 0), Decl(mod1.ts, 5, 25), Decl(mod1.ts, 8, 5))
-
-        foo(): Lib;
->foo : Symbol(Cls.foo, Decl(mod1.ts, 6, 19))
->Lib : Symbol(Lib, Decl(index.d.ts, 0, 0))
-    }
-    namespace Cls {
->Cls : Symbol(Cls, Decl(main.ts, 0, 0), Decl(mod1.ts, 5, 25), Decl(mod1.ts, 8, 5))
-
-        function bar(): Lib;
->bar : Symbol(bar, Decl(mod1.ts, 9, 19))
->Lib : Symbol(Lib, Decl(index.d.ts, 0, 0))
-    }
-}
-
diff --git a/tests/baselines/reference/typeReferenceDirectives12.types b/tests/baselines/reference/typeReferenceDirectives12.types
deleted file mode 100644
index bd429b91f1c..00000000000
--- a/tests/baselines/reference/typeReferenceDirectives12.types
+++ /dev/null
@@ -1,73 +0,0 @@
-=== /mod2.ts ===
-import { Cls } from "./main";
->Cls : typeof Cls
-
-import "./mod1";
-
-export const cls = Cls;
->cls : typeof Cls
->Cls : typeof Cls
-
-export const foo = new Cls().foo();
->foo : Lib
->new Cls().foo() : Lib
->new Cls().foo : () => Lib
->new Cls() : Cls
->Cls : typeof Cls
->foo : () => Lib
-
-export const bar = Cls.bar();
->bar : Lib
->Cls.bar() : Lib
->Cls.bar : () => Lib
->Cls : typeof Cls
->bar : () => Lib
-
-=== /types/lib/index.d.ts ===
-
-
-interface Lib { x }
->Lib : Lib
->x : any
-
-=== /main.ts ===
-export class Cls {
->Cls : Cls
-
-    x
->x : any
-}
-
-=== /mod1.ts ===
-/// <reference types="lib" />
-
-import {Cls} from "./main";
->Cls : typeof Cls
-
-Cls.prototype.foo = function() { return undefined; }
->Cls.prototype.foo = function() { return undefined; } : () => any
->Cls.prototype.foo : () => Lib
->Cls.prototype : Cls
->Cls : typeof Cls
->prototype : Cls
->foo : () => Lib
->function() { return undefined; } : () => any
->undefined : undefined
-
-declare module "./main" {
-    interface Cls {
->Cls : Cls
-
-        foo(): Lib;
->foo : () => Lib
->Lib : Lib
-    }
-    namespace Cls {
->Cls : typeof Cls
-
-        function bar(): Lib;
->bar : () => Lib
->Lib : Lib
-    }
-}
-