diff --git a/tests/baselines/reference/separateCompilationPlainFile-AMD.errors.txt b/tests/baselines/reference/separateCompilationPlainFile-AMD.errors.txt
new file mode 100644
index 00000000000..3605dc7f44e
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-AMD.errors.txt
@@ -0,0 +1,10 @@
+tests/cases/compiler/separateCompilationPlainFile-AMD.ts(2,1): error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+
+
+==== tests/cases/compiler/separateCompilationPlainFile-AMD.ts (1 errors) ====
+    
+    declare function run(a: number): void;
+    ~~~~~~~
+!!! error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+    run(1);
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/separateCompilationPlainFile-AMD.js b/tests/baselines/reference/separateCompilationPlainFile-AMD.js
new file mode 100644
index 00000000000..e3e9fc1eaeb
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-AMD.js
@@ -0,0 +1,10 @@
+//// [separateCompilationPlainFile-AMD.ts]
+
+declare function run(a: number): void;
+run(1);
+
+
+//// [separateCompilationPlainFile-AMD.js]
+define(["require", "exports"], function (require, exports) {
+    run(1);
+});
diff --git a/tests/baselines/reference/separateCompilationPlainFile-CommonJS.errors.txt b/tests/baselines/reference/separateCompilationPlainFile-CommonJS.errors.txt
new file mode 100644
index 00000000000..d56e82fd6e1
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-CommonJS.errors.txt
@@ -0,0 +1,10 @@
+tests/cases/compiler/separateCompilationPlainFile-CommonJS.ts(2,1): error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+
+
+==== tests/cases/compiler/separateCompilationPlainFile-CommonJS.ts (1 errors) ====
+    
+    declare function run(a: number): void;
+    ~~~~~~~
+!!! error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+    run(1);
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/separateCompilationPlainFile-CommonJS.js b/tests/baselines/reference/separateCompilationPlainFile-CommonJS.js
new file mode 100644
index 00000000000..cd82cdf20a6
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-CommonJS.js
@@ -0,0 +1,8 @@
+//// [separateCompilationPlainFile-CommonJS.ts]
+
+declare function run(a: number): void;
+run(1);
+
+
+//// [separateCompilationPlainFile-CommonJS.js]
+run(1);
diff --git a/tests/baselines/reference/separateCompilationPlainFile-ES6.errors.txt b/tests/baselines/reference/separateCompilationPlainFile-ES6.errors.txt
new file mode 100644
index 00000000000..6054ab552c8
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-ES6.errors.txt
@@ -0,0 +1,10 @@
+tests/cases/compiler/separateCompilationPlainFile-ES6.ts(2,1): error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+
+
+==== tests/cases/compiler/separateCompilationPlainFile-ES6.ts (1 errors) ====
+    
+    declare function run(a: number): void;
+    ~~~~~~~
+!!! error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+    run(1);
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/separateCompilationPlainFile-ES6.js b/tests/baselines/reference/separateCompilationPlainFile-ES6.js
new file mode 100644
index 00000000000..1cb6082f134
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-ES6.js
@@ -0,0 +1,8 @@
+//// [separateCompilationPlainFile-ES6.ts]
+
+declare function run(a: number): void;
+run(1);
+
+
+//// [separateCompilationPlainFile-ES6.js]
+run(1);
diff --git a/tests/baselines/reference/separateCompilationPlainFile-System.errors.txt b/tests/baselines/reference/separateCompilationPlainFile-System.errors.txt
new file mode 100644
index 00000000000..716909cee4f
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-System.errors.txt
@@ -0,0 +1,10 @@
+tests/cases/compiler/separateCompilationPlainFile-System.ts(2,1): error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+
+
+==== tests/cases/compiler/separateCompilationPlainFile-System.ts (1 errors) ====
+    
+    declare function run(a: number): void;
+    ~~~~~~~
+!!! error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+    run(1);
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/separateCompilationPlainFile-System.js b/tests/baselines/reference/separateCompilationPlainFile-System.js
new file mode 100644
index 00000000000..c256ed7862a
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-System.js
@@ -0,0 +1,15 @@
+//// [separateCompilationPlainFile-System.ts]
+
+declare function run(a: number): void;
+run(1);
+
+
+//// [separateCompilationPlainFile-System.js]
+System.register([], function(exports_1) {
+    return {
+        setters:[],
+        execute: function() {
+            run(1);
+        }
+    }
+});
diff --git a/tests/baselines/reference/separateCompilationPlainFile-UMD.errors.txt b/tests/baselines/reference/separateCompilationPlainFile-UMD.errors.txt
new file mode 100644
index 00000000000..c86daeabddf
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-UMD.errors.txt
@@ -0,0 +1,10 @@
+tests/cases/compiler/separateCompilationPlainFile-UMD.ts(2,1): error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+
+
+==== tests/cases/compiler/separateCompilationPlainFile-UMD.ts (1 errors) ====
+    
+    declare function run(a: number): void;
+    ~~~~~~~
+!!! error TS1208: Cannot compile non-external modules when the '--separateCompilation' flag is provided.
+    run(1);
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/separateCompilationPlainFile-UMD.js b/tests/baselines/reference/separateCompilationPlainFile-UMD.js
new file mode 100644
index 00000000000..6a145e7d239
--- /dev/null
+++ b/tests/baselines/reference/separateCompilationPlainFile-UMD.js
@@ -0,0 +1,17 @@
+//// [separateCompilationPlainFile-UMD.ts]
+
+declare function run(a: number): void;
+run(1);
+
+
+//// [separateCompilationPlainFile-UMD.js]
+(function (deps, 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(deps, factory);
+    }
+})(["require", "exports"], function (require, exports) {
+    run(1);
+});
diff --git a/tests/cases/compiler/separateCompilationPlainFile-AMD.ts b/tests/cases/compiler/separateCompilationPlainFile-AMD.ts
new file mode 100644
index 00000000000..a1010ce3e8c
--- /dev/null
+++ b/tests/cases/compiler/separateCompilationPlainFile-AMD.ts
@@ -0,0 +1,6 @@
+// @target: es5
+// @module: amd
+// @separateCompilation: true
+
+declare function run(a: number): void;
+run(1);
diff --git a/tests/cases/compiler/separateCompilationPlainFile-CommonJS.ts b/tests/cases/compiler/separateCompilationPlainFile-CommonJS.ts
new file mode 100644
index 00000000000..532d97f09eb
--- /dev/null
+++ b/tests/cases/compiler/separateCompilationPlainFile-CommonJS.ts
@@ -0,0 +1,6 @@
+// @target: es5
+// @module: commonjs
+// @separateCompilation: true
+
+declare function run(a: number): void;
+run(1);
diff --git a/tests/cases/compiler/separateCompilationPlainFile-ES6.ts b/tests/cases/compiler/separateCompilationPlainFile-ES6.ts
new file mode 100644
index 00000000000..20d4e8d79a2
--- /dev/null
+++ b/tests/cases/compiler/separateCompilationPlainFile-ES6.ts
@@ -0,0 +1,5 @@
+// @target: es6
+// @separateCompilation: true
+
+declare function run(a: number): void;
+run(1);
diff --git a/tests/cases/compiler/separateCompilationPlainFile-System.ts b/tests/cases/compiler/separateCompilationPlainFile-System.ts
new file mode 100644
index 00000000000..69065718254
--- /dev/null
+++ b/tests/cases/compiler/separateCompilationPlainFile-System.ts
@@ -0,0 +1,6 @@
+// @target: es5
+// @module: system
+// @separateCompilation: true
+
+declare function run(a: number): void;
+run(1);
diff --git a/tests/cases/compiler/separateCompilationPlainFile-UMD.ts b/tests/cases/compiler/separateCompilationPlainFile-UMD.ts
new file mode 100644
index 00000000000..4ab45686c90
--- /dev/null
+++ b/tests/cases/compiler/separateCompilationPlainFile-UMD.ts
@@ -0,0 +1,6 @@
+// @target: es5
+// @module: umd
+// @separateCompilation: true
+
+declare function run(a: number): void;
+run(1);