Index: lib/Tooling/Refactoring.cpp
===================================================================
--- lib/Tooling/Refactoring.cpp
+++ lib/Tooling/Refactoring.cpp
@@ -19,6 +19,8 @@
 #include "clang/Rewrite/Core/Rewriter.h"
 #include "clang/Tooling/Refactoring.h"
 #include "llvm/Support/raw_os_ostream.h"
+#include "llvm/Support/FileSystem.h"
+#include "llvm/Support/Path.h"
 
 namespace clang {
 namespace tooling {
@@ -103,7 +105,16 @@
   const std::pair<FileID, unsigned> DecomposedLocation =
       Sources.getDecomposedLoc(Start);
   const FileEntry *Entry = Sources.getFileEntryForID(DecomposedLocation.first);
-  this->FilePath = Entry != NULL ? Entry->getName() : InvalidLocation;
+
+  if (Entry != NULL) {
+    // Make FilePath absolute so replacements can be applied correctly when
+    // relative paths for files are used.
+    llvm::SmallString<256> FilePath(Entry->getName());
+    llvm::error_code EC = llvm::sys::fs::make_absolute(FilePath);
+    // Don't change the FilePath if the file is a virtual file.
+    this->FilePath = EC ? FilePath.c_str() : Entry->getName();
+  } else
+    this->FilePath = InvalidLocation;
   this->ReplacementRange = Range(DecomposedLocation.second, Length);
   this->ReplacementText = ReplacementText;
 }
Index: test/Tooling/clang-check-rel-path.cpp
===================================================================
--- /dev/null
+++ test/Tooling/clang-check-rel-path.cpp
@@ -0,0 +1,10 @@
+// This block test a compilation database with files relative to the directory
+// RUN: rm -rf %t
+// RUN: mkdir %t
+// RUN: echo '[{"directory":"%t","command":"clang++ -c test.cpp","file":"test.cpp"}]' | sed -e 's/\\/\//g' > %t/compile_commands.json
+// RUN: cp "%s" "%t/test.cpp"
+// RUN: not clang-check -p "%t" "%t/test.cpp" 2>&1|FileCheck %s
+// FIXME: Make the above easier.
+
+// CHECK: C++ requires
+invalid;