Index: include/clang/Tooling/Tooling.h
===================================================================
--- include/clang/Tooling/Tooling.h
+++ include/clang/Tooling/Tooling.h
@@ -296,10 +296,14 @@
   ///        not found in Compilations, it is skipped.
   /// \param PCHContainerOps The PCHContainerOperations for loading and creating
   /// clang modules.
+  /// \param BaseFS VFS used for all underlying file accesses when running the
+  /// tool.
   ClangTool(const CompilationDatabase &Compilations,
             ArrayRef<std::string> SourcePaths,
             std::shared_ptr<PCHContainerOperations> PCHContainerOps =
-                std::make_shared<PCHContainerOperations>());
+                std::make_shared<PCHContainerOperations>(),
+            IntrusiveRefCntPtr<vfs::FileSystem> BaseFS =
+                vfs::getRealFileSystem());
 
   ~ClangTool();
 
Index: lib/Tooling/Tooling.cpp
===================================================================
--- lib/Tooling/Tooling.cpp
+++ lib/Tooling/Tooling.cpp
@@ -328,10 +328,11 @@
 
 ClangTool::ClangTool(const CompilationDatabase &Compilations,
                      ArrayRef<std::string> SourcePaths,
-                     std::shared_ptr<PCHContainerOperations> PCHContainerOps)
+                     std::shared_ptr<PCHContainerOperations> PCHContainerOps,
+                     IntrusiveRefCntPtr<vfs::FileSystem> BaseFS)
     : Compilations(Compilations), SourcePaths(SourcePaths),
       PCHContainerOps(std::move(PCHContainerOps)),
-      OverlayFileSystem(new vfs::OverlayFileSystem(vfs::getRealFileSystem())),
+      OverlayFileSystem(new vfs::OverlayFileSystem(BaseFS)),
       InMemoryFileSystem(new vfs::InMemoryFileSystem),
       Files(new FileManager(FileSystemOptions(), OverlayFileSystem)),
       DiagConsumer(nullptr) {
Index: unittests/Tooling/ToolingTest.cpp
===================================================================
--- unittests/Tooling/ToolingTest.cpp
+++ unittests/Tooling/ToolingTest.cpp
@@ -402,6 +402,24 @@
   EXPECT_FALSE(Found);
 }
 
+TEST(ClangToolTest, BaseVirtualFileSystemUsage) {
+  FixedCompilationDatabase Compilations("/", std::vector<std::string>());
+  llvm::IntrusiveRefCntPtr<vfs::OverlayFileSystem> OverlayFileSystem(
+      new vfs::OverlayFileSystem(vfs::getRealFileSystem()));
+  llvm::IntrusiveRefCntPtr<vfs::InMemoryFileSystem> InMemoryFileSystem(
+      new vfs::InMemoryFileSystem);
+  OverlayFileSystem->pushOverlay(InMemoryFileSystem);
+
+  InMemoryFileSystem->addFile(
+      "a.cpp", 0, llvm::MemoryBuffer::getMemBuffer("int main() {}"));
+
+  ClangTool Tool(Compilations, std::vector<std::string>(1, "a.cpp"),
+                 std::make_shared<PCHContainerOperations>(), OverlayFileSystem);
+  std::unique_ptr<FrontendActionFactory> Action(
+      newFrontendActionFactory<SyntaxOnlyAction>());
+  EXPECT_EQ(0, Tool.run(Action.get()));
+}
+
 // Check getClangStripDependencyFileAdjuster doesn't strip args after -MD/-MMD.
 TEST(ClangToolTest, StripDependencyFileAdjuster) {
   FixedCompilationDatabase Compilations("/", {"-MD", "-c", "-MMD", "-w"});