Index: include/clang/Tooling/Tooling.h
===================================================================
--- include/clang/Tooling/Tooling.h
+++ include/clang/Tooling/Tooling.h
@@ -326,6 +326,9 @@
   /// Runs an action over all files specified in the command line.
   ///
   /// \param Action Tool action.
+  ///
+  /// \returns 0 on success; 1 if any error occured; 2 if there is no error but
+  /// some files are skipped due to missing compile commands.
   int run(ToolAction *Action);
 
   /// \brief Create an AST for each file specified in the command line and
Index: lib/Tooling/Tooling.cpp
===================================================================
--- lib/Tooling/Tooling.cpp
+++ lib/Tooling/Tooling.cpp
@@ -387,6 +387,7 @@
             llvm::MemoryBuffer::getMemBuffer(MappedFile.second));
 
   bool ProcessingFailed = false;
+  bool FileSkipped = false;
   for (const auto &SourcePath : SourcePaths) {
     std::string File(getAbsolutePath(SourcePath));
 
@@ -406,6 +407,7 @@
       // specify all files I want to run over explicitly, where this should
       // be an error. We'll want to add an option for this.
       llvm::errs() << "Skipping " << File << ". Compile command not found.\n";
+      FileSkipped = true;
       continue;
     }
     for (CompileCommand &CompileCommand : CompileCommandsForFile) {
@@ -465,7 +467,7 @@
                                  Twine(InitialDirectory) + "\n!");
     }
   }
-  return ProcessingFailed ? 1 : 0;
+  return ProcessingFailed ? 1 : (FileSkipped ? 2 : 0);
 }
 
 namespace {