Index: clang/lib/Frontend/CompilerInvocation.cpp
===================================================================
--- clang/lib/Frontend/CompilerInvocation.cpp
+++ clang/lib/Frontend/CompilerInvocation.cpp
@@ -1566,7 +1566,14 @@
     frontend::IncludeDirGroup Group = frontend::System;
     if (A->getOption().matches(OPT_internal_externc_isystem))
       Group = frontend::ExternCSystem;
-    Opts.AddPath(A->getValue(), Group, false, true);
+
+    SmallString<128> P(Opts.ResourceDir);
+    llvm::sys::path::append(P, "include");
+
+    if (StringRef(A->getValue()) == P)
+      Opts.AddPath(A->getValue(), Group, false, true);
+    else
+      Opts.AddPath(A->getValue(), Group, false, false);
   }
 
   // Add the path prefixes which are implicitly treated as being system headers.
Index: clang/test/Driver/sysroot-flags.c
===================================================================
--- clang/test/Driver/sysroot-flags.c
+++ clang/test/Driver/sysroot-flags.c
@@ -26,3 +26,7 @@
 // RUN:   FileCheck %s -check-prefix=SYSROOT_SEPARATE
 // SYSROOT_SEPARATE: "-isysroot" "{{[^"]*}}/foo/bar"
 // SYSROOT_SEPARATE: "--sysroot{{" "|=}}{{[^"]*}}/foo/bar"
+
+// Check that -isysroot is handled properly
+// RUN: %clang -isysroot /foo/bar -c %s -v 2>&1 | \
+// RUN:   grep "/foo/bar"