Index: cfe/trunk/lib/Serialization/ASTReader.cpp
===================================================================
--- cfe/trunk/lib/Serialization/ASTReader.cpp
+++ cfe/trunk/lib/Serialization/ASTReader.cpp
@@ -1950,15 +1950,13 @@
   Module *PrevOwner = nullptr;
   if (SubmoduleID PrevModID = PrevMI->getOwningModuleID())
     PrevOwner = Reader.getSubmodule(PrevModID);
-  SourceManager &SrcMgr = Reader.getSourceManager();
-  bool PrevInSystem
-    = PrevOwner? PrevOwner->IsSystem
-               : SrcMgr.isInSystemHeader(PrevMI->getDefinitionLoc());
-  bool NewInSystem
-    = NewOwner? NewOwner->IsSystem
-              : SrcMgr.isInSystemHeader(NewMI->getDefinitionLoc());
   if (PrevOwner && PrevOwner == NewOwner)
     return false;
+  SourceManager &SrcMgr = Reader.getSourceManager();
+  bool PrevInSystem = (PrevOwner && PrevOwner->IsSystem) ||
+                      SrcMgr.isInSystemHeader(PrevMI->getDefinitionLoc());
+  bool NewInSystem = (NewOwner && NewOwner->IsSystem) ||
+                     SrcMgr.isInSystemHeader(NewMI->getDefinitionLoc());
   return PrevInSystem && NewInSystem;
 }
 
Index: cfe/trunk/test/Modules/Inputs/macro-ambiguity/a/quote/a_quote.h
===================================================================
--- cfe/trunk/test/Modules/Inputs/macro-ambiguity/a/quote/a_quote.h
+++ cfe/trunk/test/Modules/Inputs/macro-ambiguity/a/quote/a_quote.h
@@ -0,0 +1,8 @@
+#ifndef A_QUOTE_H
+#define A_QUOTE_H
+
+#define FOO1_QUOTE(x) x + x
+#define BAR1_QUOTE(x) x + x
+#define BAZ1_QUOTE(x) x + x
+
+#endif
Index: cfe/trunk/test/Modules/Inputs/macro-ambiguity/a/system/a_system.h
===================================================================
--- cfe/trunk/test/Modules/Inputs/macro-ambiguity/a/system/a_system.h
+++ cfe/trunk/test/Modules/Inputs/macro-ambiguity/a/system/a_system.h
@@ -0,0 +1,15 @@
+#ifndef A_SYSTEM_H
+#define A_SYSTEM_H
+
+// FIXME: We have to use this to mark the header as a system header in
+// a module because header search didn't actually occur and so we can't have
+// found the header via system header search, even though when we map to this
+// header and load the module we will have mapped to the header by finding it
+// via system header search.
+#pragma GCC system_header
+
+#define FOO1_SYSTEM(x) x + x
+#define BAR1_SYSTEM(x) x + x
+#define BAZ1_SYSTEM(x) x + x
+
+#endif
Index: cfe/trunk/test/Modules/Inputs/macro-ambiguity/b/quote/b_quote.h
===================================================================
--- cfe/trunk/test/Modules/Inputs/macro-ambiguity/b/quote/b_quote.h
+++ cfe/trunk/test/Modules/Inputs/macro-ambiguity/b/quote/b_quote.h
@@ -0,0 +1,8 @@
+#ifndef B_QUOTE_H
+#define B_QUOTE_H
+
+#define FOO2_QUOTE(x) x + x
+#define BAR2_QUOTE(x) x + x
+#define BAZ2_QUOTE(x) x + x
+
+#endif
Index: cfe/trunk/test/Modules/Inputs/macro-ambiguity/b/system/b_system.h
===================================================================
--- cfe/trunk/test/Modules/Inputs/macro-ambiguity/b/system/b_system.h
+++ cfe/trunk/test/Modules/Inputs/macro-ambiguity/b/system/b_system.h
@@ -0,0 +1,15 @@
+#ifndef B_SYSTEM_H
+#define B_SYSTEM_H
+
+// FIXME: We have to use this to mark the header as a system header in
+// a module because header search didn't actually occur and so we can't have
+// found the header via system header search, even though when we map to this
+// header and load the module we will have mapped to the header by finding it
+// via system header search.
+#pragma GCC system_header
+
+#define FOO2_SYSTEM(x) x + x
+#define BAR2_SYSTEM(x) x + x
+#define BAZ2_SYSTEM(x) x + x
+
+#endif
Index: cfe/trunk/test/Modules/Inputs/macro-ambiguity/c/quote/c_quote.h
===================================================================
--- cfe/trunk/test/Modules/Inputs/macro-ambiguity/c/quote/c_quote.h
+++ cfe/trunk/test/Modules/Inputs/macro-ambiguity/c/quote/c_quote.h
@@ -0,0 +1,7 @@
+#ifndef C_QUOTE_H
+#define C_QUOTE_H
+
+#define FOO1_QUOTE(x) 2 * x
+#define FOO2_QUOTE(x) 2 * x
+
+#endif
Index: cfe/trunk/test/Modules/Inputs/macro-ambiguity/c/system/c_system.h
===================================================================
--- cfe/trunk/test/Modules/Inputs/macro-ambiguity/c/system/c_system.h
+++ cfe/trunk/test/Modules/Inputs/macro-ambiguity/c/system/c_system.h
@@ -0,0 +1,14 @@
+#ifndef C_SYSTEM_H
+#define C_SYSTEM_H
+
+// FIXME: We have to use this to mark the header as a system header in
+// a module because header search didn't actually occur and so we can't have
+// found the header via system header search, even though when we map to this
+// header and load the module we will have mapped to the header by finding it
+// via system header search.
+#pragma GCC system_header
+
+#define FOO1_SYSTEM(x) 2 * x
+#define FOO2_SYSTEM(x) 2 * x
+
+#endif
Index: cfe/trunk/test/Modules/Inputs/macro-ambiguity/d/quote/d_quote.h
===================================================================
--- cfe/trunk/test/Modules/Inputs/macro-ambiguity/d/quote/d_quote.h
+++ cfe/trunk/test/Modules/Inputs/macro-ambiguity/d/quote/d_quote.h
@@ -0,0 +1,7 @@
+#ifndef D_QUOTE_H
+#define D_QUOTE_H
+
+#define BAR1_QUOTE(x) 2 * x
+#define BAR2_QUOTE(x) 2 * x
+
+#endif
Index: cfe/trunk/test/Modules/Inputs/macro-ambiguity/d/system/d_system.h
===================================================================
--- cfe/trunk/test/Modules/Inputs/macro-ambiguity/d/system/d_system.h
+++ cfe/trunk/test/Modules/Inputs/macro-ambiguity/d/system/d_system.h
@@ -0,0 +1,14 @@
+#ifndef D_SYSTEM_H
+#define D_SYSTEM_H
+
+// FIXME: We have to use this to mark the header as a system header in
+// a module because header search didn't actually occur and so we can't have
+// found the header via system header search, even though when we map to this
+// header and load the module we will have mapped to the header by finding it
+// via system header search.
+#pragma GCC system_header
+
+#define BAR1_SYSTEM(x) 2 * x
+#define BAR2_SYSTEM(x) 2 * x
+
+#endif
Index: cfe/trunk/test/Modules/Inputs/macro-ambiguity/e/quote/e_quote.h
===================================================================
--- cfe/trunk/test/Modules/Inputs/macro-ambiguity/e/quote/e_quote.h
+++ cfe/trunk/test/Modules/Inputs/macro-ambiguity/e/quote/e_quote.h
@@ -0,0 +1,7 @@
+#ifndef E_QUOTE_H
+#define E_QUOTE_H
+
+#define BAZ1_QUOTE(x) 2 * x
+#define BAZ2_QUOTE(x) 2 * x
+
+#endif
Index: cfe/trunk/test/Modules/Inputs/macro-ambiguity/e/system/e_system.h
===================================================================
--- cfe/trunk/test/Modules/Inputs/macro-ambiguity/e/system/e_system.h
+++ cfe/trunk/test/Modules/Inputs/macro-ambiguity/e/system/e_system.h
@@ -0,0 +1,7 @@
+#ifndef E_SYSTEM_H
+#define E_SYSTEM_H
+
+#define BAZ1_SYSTEM(x) 2 * x
+#define BAZ2_SYSTEM(x) 2 * x
+
+#endif
Index: cfe/trunk/test/Modules/Inputs/macro-ambiguity/module.modulemap
===================================================================
--- cfe/trunk/test/Modules/Inputs/macro-ambiguity/module.modulemap
+++ cfe/trunk/test/Modules/Inputs/macro-ambiguity/module.modulemap
@@ -0,0 +1,25 @@
+module a {
+  header "Inputs/macro-ambiguity/a/quote/a_quote.h"
+  header "Inputs/macro-ambiguity/a/system/a_system.h"
+  export *
+}
+module b [system] {
+  header "Inputs/macro-ambiguity/b/quote/b_quote.h"
+  header "Inputs/macro-ambiguity/b/system/b_system.h"
+  export *
+}
+module c {
+  header "Inputs/macro-ambiguity/c/quote/c_quote.h"
+  header "Inputs/macro-ambiguity/c/system/c_system.h"
+  export *
+}
+module d [system] {
+  header "Inputs/macro-ambiguity/d/quote/d_quote.h"
+  header "Inputs/macro-ambiguity/d/system/d_system.h"
+  export *
+}
+module e {
+  textual header "Inputs/macro-ambiguity/e/quote/e_quote.h"
+  textual header "Inputs/macro-ambiguity/e/system/e_system.h"
+  export *
+}
Index: cfe/trunk/test/Modules/macro-ambiguity.cpp
===================================================================
--- cfe/trunk/test/Modules/macro-ambiguity.cpp
+++ cfe/trunk/test/Modules/macro-ambiguity.cpp
@@ -0,0 +1,115 @@
+// RUN: rm -rf %t
+// RUN: cd %S
+//
+// RUN: %clang_cc1 -fmodules -x c++ -fmodules-cache-path=%t \
+// RUN:   -v \
+// RUN:   -iquote Inputs/macro-ambiguity/a/quote \
+// RUN:   -isystem Inputs/macro-ambiguity/a/system \
+// RUN:   -fno-implicit-modules -fno-modules-implicit-maps \
+// RUN:   -fmodule-map-file-home-is-cwd \
+// RUN:   -emit-module -fmodule-name=a -o %t/a.pcm \
+// RUN:   Inputs/macro-ambiguity/module.modulemap
+//
+// RUN: %clang_cc1 -fmodules -x c++ -fmodules-cache-path=%t \
+// RUN:   -v \
+// RUN:   -iquote Inputs/macro-ambiguity/b/quote \
+// RUN:   -isystem Inputs/macro-ambiguity/b/system \
+// RUN:   -fno-implicit-modules -fno-modules-implicit-maps \
+// RUN:   -fmodule-map-file-home-is-cwd \
+// RUN:   -emit-module -fmodule-name=b -o %t/b.pcm \
+// RUN:   Inputs/macro-ambiguity/module.modulemap
+//
+// RUN: %clang_cc1 -fmodules -x c++ -fmodules-cache-path=%t \
+// RUN:   -v \
+// RUN:   -iquote Inputs/macro-ambiguity/c/quote \
+// RUN:   -isystem Inputs/macro-ambiguity/c/system \
+// RUN:   -fno-implicit-modules -fno-modules-implicit-maps \
+// RUN:   -fmodule-map-file-home-is-cwd \
+// RUN:   -emit-module -fmodule-name=c -o %t/c.pcm \
+// RUN:   Inputs/macro-ambiguity/module.modulemap
+//
+// RUN: %clang_cc1 -fmodules -x c++ -fmodules-cache-path=%t \
+// RUN:   -v \
+// RUN:   -iquote Inputs/macro-ambiguity/d/quote \
+// RUN:   -isystem Inputs/macro-ambiguity/d/system \
+// RUN:   -fno-implicit-modules -fno-modules-implicit-maps \
+// RUN:   -fmodule-map-file-home-is-cwd \
+// RUN:   -emit-module -fmodule-name=d -o %t/d.pcm \
+// RUN:   Inputs/macro-ambiguity/module.modulemap
+//
+// RUN: %clang_cc1 -fmodules -x c++ -fmodules-cache-path=%t \
+// RUN:   -v \
+// RUN:   -iquote Inputs/macro-ambiguity/a/quote \
+// RUN:   -isystem Inputs/macro-ambiguity/a/system \
+// RUN:   -iquote Inputs/macro-ambiguity/b/quote \
+// RUN:   -isystem Inputs/macro-ambiguity/b/system \
+// RUN:   -iquote Inputs/macro-ambiguity/c/quote \
+// RUN:   -isystem Inputs/macro-ambiguity/c/system \
+// RUN:   -iquote Inputs/macro-ambiguity/d/quote \
+// RUN:   -isystem Inputs/macro-ambiguity/d/system \
+// RUN:   -iquote Inputs/macro-ambiguity/e/quote \
+// RUN:   -isystem Inputs/macro-ambiguity/e/system \
+// RUN:   -fno-implicit-modules -fno-modules-implicit-maps \
+// RUN:   -fmodule-map-file-home-is-cwd \
+// RUN:   -fmodule-map-file=Inputs/macro-ambiguity/module.modulemap \
+// RUN:   -fmodule-file=%t/a.pcm \
+// RUN:   -fmodule-file=%t/b.pcm \
+// RUN:   -fmodule-file=%t/c.pcm \
+// RUN:   -fmodule-file=%t/d.pcm \
+// RUN:   -Wambiguous-macro -verify macro-ambiguity.cpp
+
+// Include the textual headers first to maximize the ways in which things can
+// become ambiguous.
+#include "e_quote.h"
+#include <e_system.h>
+
+#include "a_quote.h"
+#include <a_system.h>
+#include "b_quote.h"
+#include <b_system.h>
+#include "c_quote.h"
+#include <c_system.h>
+#include "d_quote.h"
+#include <d_system.h>
+
+int test(int x) {
+  // We expect to get warnings for all of the quoted includes but none of the
+  // system includes here because the first module is a non-system module and
+  // the quote macros come from non-system-headers.
+  x = FOO1_QUOTE(x); // expected-warning {{ambiguous expansion of macro}}
+  // expected-note@Inputs/macro-ambiguity/c/quote/c_quote.h:4 {{expanding this definition}}
+  // expected-note@Inputs/macro-ambiguity/a/quote/a_quote.h:4 {{other definition}}
+
+  x = FOO1_SYSTEM(x);
+
+  x = BAR1_QUOTE(x); // expected-warning {{ambiguous expansion of macro}}
+  // expected-note@Inputs/macro-ambiguity/d/quote/d_quote.h:4 {{expanding this definition}}
+  // expected-note@Inputs/macro-ambiguity/a/quote/a_quote.h:5 {{other definition}}
+
+  x = BAR1_SYSTEM(x);
+
+  x = BAZ1_QUOTE(x); // expected-warning {{ambiguous expansion of macro}}
+  // expected-note@Inputs/macro-ambiguity/a/quote/a_quote.h:6 {{expanding this definition}}
+  // expected-note@Inputs/macro-ambiguity/e/quote/e_quote.h:4 {{other definition}}
+
+  x = BAZ1_SYSTEM(x);
+
+  // Here, we don't even warn on bar because in that cas both b and d are
+  // system modules and so the use of non-system headers is irrelevant.
+  x = FOO2_QUOTE(x); // expected-warning {{ambiguous expansion of macro}}
+  // expected-note@Inputs/macro-ambiguity/c/quote/c_quote.h:5 {{expanding this definition}}
+  // expected-note@Inputs/macro-ambiguity/b/quote/b_quote.h:4 {{other definition}}
+
+  x = FOO2_SYSTEM(x);
+
+  x = BAR2_QUOTE(x);
+
+  x = BAR2_SYSTEM(x);
+
+  x = BAZ2_QUOTE(x); // expected-warning {{ambiguous expansion of macro}}
+  // expected-note@Inputs/macro-ambiguity/b/quote/b_quote.h:6 {{expanding this definition}}
+  // expected-note@Inputs/macro-ambiguity/e/quote/e_quote.h:5 {{other definition}}
+
+  x = BAZ2_SYSTEM(x);
+  return x;
+}