diff --git a/src/compiler/commandLineParser.ts b/src/compiler/commandLineParser.ts
index 3ebb865a64c32..9478f4504b7f8 100644
--- a/src/compiler/commandLineParser.ts
+++ b/src/compiler/commandLineParser.ts
@@ -1895,7 +1895,8 @@ namespace ts {
                     filesSpecs = <ReadonlyArray<string>>raw.files;
                     const hasReferences = hasProperty(raw, "references") && !isNullOrUndefined(raw.references);
                     const hasZeroOrNoReferences = !hasReferences || raw.references.length === 0;
-                    if (filesSpecs.length === 0 && hasZeroOrNoReferences) {
+                    const hasExtends = hasProperty(raw, "extends");
+                    if (filesSpecs.length === 0 && hasZeroOrNoReferences && !hasExtends) {
                         if (sourceFile) {
                             const fileName = configFileName || "tsconfig.json";
                             const diagnosticMessage = Diagnostics.The_files_list_in_config_file_0_is_empty;
diff --git a/src/testRunner/unittests/configurationExtension.ts b/src/testRunner/unittests/configurationExtension.ts
index b9567b3b54d39..fbb4950b9a5b8 100644
--- a/src/testRunner/unittests/configurationExtension.ts
+++ b/src/testRunner/unittests/configurationExtension.ts
@@ -96,6 +96,11 @@ namespace ts {
                         include: null,
                         files: ["../main.ts"]
                     }),
+                    "dev/configs/fifth.json": JSON.stringify({
+                        extends: "./fourth",
+                        include: ["../tests/utils.ts"],
+                        files: []
+                    }),
                     "dev/extends.json": JSON.stringify({ extends: 42 }),
                     "dev/extends2.json": JSON.stringify({ extends: "configs/base" }),
                     "dev/main.ts": "",
@@ -245,6 +250,15 @@ namespace ts {
                     combinePaths(basePath, "main.ts")
                 ]);
 
+                testSuccess("can overwrite top-level files using extended []", "configs/fifth.json", {
+                    allowJs: true,
+                    noImplicitAny: true,
+                    strictNullChecks: true,
+                    module: ModuleKind.System
+                }, [
+                    combinePaths(basePath, "tests/utils.ts")
+                ]);
+
                 it("adds extendedSourceFiles only once", () => {
                     const sourceFile = readJsonConfigFile("configs/fourth.json", (path) => host.readFile(path));
                     const dir = combinePaths(basePath, "configs");