Index: clang-tidy/llvm/IncludeOrderCheck.cpp
===================================================================
--- clang-tidy/llvm/IncludeOrderCheck.cpp
+++ clang-tidy/llvm/IncludeOrderCheck.cpp
@@ -73,6 +73,9 @@
     SourceLocation HashLoc, const Token &IncludeTok, StringRef FileName,
     bool IsAngled, CharSourceRange FilenameRange, const FileEntry *File,
     StringRef SearchPath, StringRef RelativePath, const Module *Imported) {
+  if (SM.getFileID(HashLoc) != SM.getMainFileID())
+    return;
+
   // We recognize the first include as a special main module header and want
   // to leave it in the top position.
   IncludeDirective ID = {HashLoc, FilenameRange, FileName, IsAngled, false};
Index: test/clang-tidy/Inputs/Headers/cross-file-c.h
===================================================================
--- /dev/null
+++ test/clang-tidy/Inputs/Headers/cross-file-c.h
@@ -0,0 +1,2 @@
+
+#include "cross-file-b.h"
Index: test/clang-tidy/llvm-include-order.cpp
===================================================================
--- test/clang-tidy/llvm-include-order.cpp
+++ test/clang-tidy/llvm-include-order.cpp
@@ -35,3 +35,8 @@
 
 // CHECK-FIXES: #include "a.h"
 // CHECK-FIXES-NEXT: #include "b.h"
+
+// CHECK-MESSAGES-NOT: [[@LINE+1]]:1: warning: #includes are not sorted properly
+#include "cross-file-a.h"
+
+#include "cross-file-c.h"