diff --git a/src/harness/compilerRunner.ts b/src/harness/compilerRunner.ts
index 848f229f109..f7bb23527dd 100644
--- a/src/harness/compilerRunner.ts
+++ b/src/harness/compilerRunner.ts
@@ -45,14 +45,10 @@ class CompilerBaselineRunner extends RunnerBase {
             // Mocha holds onto the closure environment of the describe callback even after the test is done.
             // Everything declared here should be cleared out in the "after" callback.
             let justName: string;
-            let content: string;
-            let testCaseContent: { settings: Harness.TestCaseParser.CompilerSettings; testUnitData: Harness.TestCaseParser.TestUnitData[]; };
 
-            let units: Harness.TestCaseParser.TestUnitData[];
             let tcSettings: Harness.TestCaseParser.CompilerSettings;
 
             let lastUnit: Harness.TestCaseParser.TestUnitData;
-            let rootDir: string;
 
             let result: Harness.Compiler.CompilerResult;
             let program: ts.Program;
@@ -65,12 +61,12 @@ class CompilerBaselineRunner extends RunnerBase {
 
             before(() => {
                 justName = fileName.replace(/^.*[\\\/]/, ""); // strips the fileName from the path.
-                content = Harness.IO.readFile(fileName);
-                testCaseContent = Harness.TestCaseParser.makeUnitsFromTest(content, fileName);
-                units = testCaseContent.testUnitData;
+                const content = Harness.IO.readFile(fileName);
+                const testCaseContent = Harness.TestCaseParser.makeUnitsFromTest(content, fileName);
+                const units = testCaseContent.testUnitData;
                 tcSettings = testCaseContent.settings;
                 lastUnit = units[units.length - 1];
-                rootDir = lastUnit.originalFilePath.indexOf("conformance") === -1 ? "tests/cases/compiler/" : lastUnit.originalFilePath.substring(0, lastUnit.originalFilePath.lastIndexOf("/")) + "/";
+                const rootDir = lastUnit.originalFilePath.indexOf("conformance") === -1 ? "tests/cases/compiler/" : lastUnit.originalFilePath.substring(0, lastUnit.originalFilePath.lastIndexOf("/")) + "/";
                 harnessCompiler = Harness.Compiler.getCompiler();
                 // We need to assemble the list of input files for the compiler and other related files on the 'filesystem' (ie in a multi-file test)
                 // If the last file in a test uses require or a triple slash reference we'll assume all other files will be brought in via references,
@@ -78,16 +74,16 @@ class CompilerBaselineRunner extends RunnerBase {
                 toBeCompiled = [];
                 otherFiles = [];
                 if (/require\(/.test(lastUnit.content) || /reference\spath/.test(lastUnit.content)) {
-                    toBeCompiled.push({ unitName: rootDir + lastUnit.name, content: lastUnit.content });
+                    toBeCompiled.push({ unitName: ts.isRootedDiskPath(lastUnit.name) ? lastUnit.name : rootDir + lastUnit.name, content: lastUnit.content });
                     units.forEach(unit => {
                         if (unit.name !== lastUnit.name) {
-                            otherFiles.push({ unitName: rootDir + unit.name, content: unit.content });
+                            otherFiles.push({ unitName: ts.isRootedDiskPath(unit.name) ? unit.name : rootDir + unit.name, content: unit.content });
                         }
                     });
                 }
                 else {
                     toBeCompiled = units.map(unit => {
-                        return { unitName: rootDir + unit.name, content: unit.content };
+                        return { unitName: ts.isRootedDiskPath(unit.name) ? unit.name : rootDir + unit.name, content: unit.content };
                     });
                 }
 
@@ -104,12 +100,8 @@ class CompilerBaselineRunner extends RunnerBase {
                 // Mocha holds onto the closure environment of the describe callback even after the test is done.
                 // Therefore we have to clean out large objects after the test is done.
                 justName = undefined;
-                content = undefined;
-                testCaseContent = undefined;
-                units = undefined;
                 tcSettings = undefined;
                 lastUnit = undefined;
-                rootDir = undefined;
                 result = undefined;
                 program = undefined;
                 options = undefined;
diff --git a/tests/baselines/reference/commonSourceDir1.js b/tests/baselines/reference/commonSourceDir1.js
new file mode 100644
index 00000000000..68833aed49d
--- /dev/null
+++ b/tests/baselines/reference/commonSourceDir1.js
@@ -0,0 +1,13 @@
+//// [tests/cases/compiler/commonSourceDir1.ts] ////
+
+//// [bar.ts]
+var x: number;
+
+//// [baz.ts]
+var y: number;
+
+
+//// [bar.js]
+var x;
+//// [baz.js]
+var y;
diff --git a/tests/baselines/reference/commonSourceDir1.symbols b/tests/baselines/reference/commonSourceDir1.symbols
new file mode 100644
index 00000000000..9248e0c97af
--- /dev/null
+++ b/tests/baselines/reference/commonSourceDir1.symbols
@@ -0,0 +1,8 @@
+=== A:/foo/bar.ts ===
+var x: number;
+>x : Symbol(x, Decl(bar.ts, 0, 3))
+
+=== A:/foo/baz.ts ===
+var y: number;
+>y : Symbol(y, Decl(baz.ts, 0, 3))
+
diff --git a/tests/baselines/reference/commonSourceDir1.types b/tests/baselines/reference/commonSourceDir1.types
new file mode 100644
index 00000000000..6c9864c02cc
--- /dev/null
+++ b/tests/baselines/reference/commonSourceDir1.types
@@ -0,0 +1,8 @@
+=== A:/foo/bar.ts ===
+var x: number;
+>x : number
+
+=== A:/foo/baz.ts ===
+var y: number;
+>y : number
+
diff --git a/tests/baselines/reference/commonSourceDir2.errors.txt b/tests/baselines/reference/commonSourceDir2.errors.txt
new file mode 100644
index 00000000000..85bcf5d9c72
--- /dev/null
+++ b/tests/baselines/reference/commonSourceDir2.errors.txt
@@ -0,0 +1,9 @@
+error TS5009: Cannot find the common subdirectory path for the input files.
+
+
+!!! error TS5009: Cannot find the common subdirectory path for the input files.
+==== A:/foo/bar.ts (0 errors) ====
+    var x: number;
+    
+==== B:/foo/baz.ts (0 errors) ====
+    var y: number;
\ No newline at end of file
diff --git a/tests/baselines/reference/commonSourceDir2.js b/tests/baselines/reference/commonSourceDir2.js
new file mode 100644
index 00000000000..cf263b51fb6
--- /dev/null
+++ b/tests/baselines/reference/commonSourceDir2.js
@@ -0,0 +1,12 @@
+//// [tests/cases/compiler/commonSourceDir2.ts] ////
+
+//// [bar.ts]
+var x: number;
+
+//// [baz.ts]
+var y: number;
+
+//// [bar.js]
+var x;
+//// [baz.js]
+var y;
diff --git a/tests/baselines/reference/commonSourceDir3.js b/tests/baselines/reference/commonSourceDir3.js
new file mode 100644
index 00000000000..0535d51f4bf
--- /dev/null
+++ b/tests/baselines/reference/commonSourceDir3.js
@@ -0,0 +1,12 @@
+//// [tests/cases/compiler/commonSourceDir3.ts] ////
+
+//// [bar.ts]
+var x: number;
+
+//// [baz.ts]
+var y: number;
+
+//// [bar.js]
+var x;
+//// [baz.js]
+var y;
diff --git a/tests/baselines/reference/commonSourceDir3.symbols b/tests/baselines/reference/commonSourceDir3.symbols
new file mode 100644
index 00000000000..b8783523dfd
--- /dev/null
+++ b/tests/baselines/reference/commonSourceDir3.symbols
@@ -0,0 +1,8 @@
+=== A:/foo/bar.ts ===
+var x: number;
+>x : Symbol(x, Decl(bar.ts, 0, 3))
+
+=== a:/foo/baz.ts ===
+var y: number;
+>y : Symbol(y, Decl(baz.ts, 0, 3))
+
diff --git a/tests/baselines/reference/commonSourceDir3.types b/tests/baselines/reference/commonSourceDir3.types
new file mode 100644
index 00000000000..a0b95275897
--- /dev/null
+++ b/tests/baselines/reference/commonSourceDir3.types
@@ -0,0 +1,8 @@
+=== A:/foo/bar.ts ===
+var x: number;
+>x : number
+
+=== a:/foo/baz.ts ===
+var y: number;
+>y : number
+
diff --git a/tests/baselines/reference/commonSourceDir4.errors.txt b/tests/baselines/reference/commonSourceDir4.errors.txt
new file mode 100644
index 00000000000..f3493504e4d
--- /dev/null
+++ b/tests/baselines/reference/commonSourceDir4.errors.txt
@@ -0,0 +1,9 @@
+error TS5009: Cannot find the common subdirectory path for the input files.
+
+
+!!! error TS5009: Cannot find the common subdirectory path for the input files.
+==== A:/foo/bar.ts (0 errors) ====
+    var x: number;
+    
+==== a:/foo/baz.ts (0 errors) ====
+    var y: number;
\ No newline at end of file
diff --git a/tests/baselines/reference/commonSourceDir4.js b/tests/baselines/reference/commonSourceDir4.js
new file mode 100644
index 00000000000..2f2af9f68b2
--- /dev/null
+++ b/tests/baselines/reference/commonSourceDir4.js
@@ -0,0 +1,12 @@
+//// [tests/cases/compiler/commonSourceDir4.ts] ////
+
+//// [bar.ts]
+var x: number;
+
+//// [baz.ts]
+var y: number;
+
+//// [bar.js]
+var x;
+//// [baz.js]
+var y;
diff --git a/tests/cases/compiler/commonSourceDir1.ts b/tests/cases/compiler/commonSourceDir1.ts
new file mode 100644
index 00000000000..1a178ac0226
--- /dev/null
+++ b/tests/cases/compiler/commonSourceDir1.ts
@@ -0,0 +1,6 @@
+// @outDir: A:/
+// @Filename: A:/foo/bar.ts
+var x: number;
+
+// @Filename: A:/foo/baz.ts
+var y: number;
diff --git a/tests/cases/compiler/commonSourceDir2.ts b/tests/cases/compiler/commonSourceDir2.ts
new file mode 100644
index 00000000000..68dab0727a3
--- /dev/null
+++ b/tests/cases/compiler/commonSourceDir2.ts
@@ -0,0 +1,6 @@
+// @outDir: A:/
+// @Filename: A:/foo/bar.ts
+var x: number;
+
+// @Filename: B:/foo/baz.ts
+var y: number;
\ No newline at end of file
diff --git a/tests/cases/compiler/commonSourceDir3.ts b/tests/cases/compiler/commonSourceDir3.ts
new file mode 100644
index 00000000000..cc42eb8f267
--- /dev/null
+++ b/tests/cases/compiler/commonSourceDir3.ts
@@ -0,0 +1,6 @@
+// @outDir: A:/
+// @Filename: A:/foo/bar.ts
+var x: number;
+
+// @Filename: a:/foo/baz.ts
+var y: number;
\ No newline at end of file
diff --git a/tests/cases/compiler/commonSourceDir4.ts b/tests/cases/compiler/commonSourceDir4.ts
new file mode 100644
index 00000000000..41ee7a0344a
--- /dev/null
+++ b/tests/cases/compiler/commonSourceDir4.ts
@@ -0,0 +1,7 @@
+// @useCaseSensitiveFileNames: true
+// @outDir: A:/
+// @Filename: A:/foo/bar.ts
+var x: number;
+
+// @Filename: a:/foo/baz.ts
+var y: number;
\ No newline at end of file