Index: clang-tidy/ClangTidyDiagnosticConsumer.cpp
===================================================================
--- clang-tidy/ClangTidyDiagnosticConsumer.cpp
+++ clang-tidy/ClangTidyDiagnosticConsumer.cpp
@@ -469,34 +469,40 @@
   }
 
   // Build events from error intervals.
-  std::vector<Event> Events;
+  std::map<std::string, std::vector<Event>> FileEvents;
   for (unsigned I = 0; I < Errors.size(); ++I) {
     for (const auto &Replace : Errors[I].Fix) {
       unsigned Begin = Replace.getOffset();
       unsigned End = Begin + Replace.getLength();
+      const std::string &FilePath = Replace.getFilePath();
       // FIXME: Handle empty intervals, such as those from insertions.
       if (Begin == End)
         continue;
-      Events.push_back(Event(Begin, End, Event::ET_Begin, I, Sizes[I]));
-      Events.push_back(Event(Begin, End, Event::ET_End, I, Sizes[I]));
+      FileEvents[FilePath].push_back(
+          Event(Begin, End, Event::ET_Begin, I, Sizes[I]));
+      FileEvents[FilePath].push_back(
+          Event(Begin, End, Event::ET_End, I, Sizes[I]));
     }
   }
-  std::sort(Events.begin(), Events.end());
 
-  // Sweep.
   std::vector<bool> Apply(Errors.size(), true);
-  int OpenIntervals = 0;
-  for (const auto &Event : Events) {
-    if (Event.Type == Event::ET_End)
-      --OpenIntervals;
-    // This has to be checked after removing the interval from the count if it
-    // is an end event, or before adding it if it is a begin event.
-    if (OpenIntervals != 0)
-      Apply[Event.ErrorId] = false;
-    if (Event.Type == Event::ET_Begin)
-      ++OpenIntervals;
+  for (auto &FileAndEvents : FileEvents) {
+    std::vector<Event> &Events = FileAndEvents.second;
+    // Sweep.
+    std::sort(Events.begin(), Events.end());
+    int OpenIntervals = 0;
+    for (const auto &Event : Events) {
+      if (Event.Type == Event::ET_End)
+        --OpenIntervals;
+      // This has to be checked after removing the interval from the count if it
+      // is an end event, or before adding it if it is a begin event.
+      if (OpenIntervals != 0)
+        Apply[Event.ErrorId] = false;
+      if (Event.Type == Event::ET_Begin)
+        ++OpenIntervals;
+    }
+    assert(OpenIntervals == 0 && "Amount of begin/end points doesn't match");
   }
-  assert(OpenIntervals == 0 && "Amount of begin/end points doesn't match");
 
   for (unsigned I = 0; I < Errors.size(); ++I) {
     if (!Apply[I]) {
Index: test/clang-tidy/Inputs/overlapping/o.h
===================================================================
--- /dev/null
+++ test/clang-tidy/Inputs/overlapping/o.h
@@ -0,0 +1,9 @@
+// run: ! clang-tidy -checks=-*,llvm-include-order -header-filter=.* %s \
+// run:   -- -isystem %S/Inputs/Headers -I %S/Inputs/overlapping | \
+// run:   grep "note: this fix will not be applied because it overlaps with another fix"
+
+#include "b.h"
+#include "a.h"
+
+// The comments above are there to match the offset of the #include with the
+// offset of the #includes in the .cpp file.
Index: test/clang-tidy/overlapping.cpp
===================================================================
--- /dev/null
+++ test/clang-tidy/overlapping.cpp
@@ -0,0 +1,10 @@
+// RUN: ! clang-tidy -checks=-*,llvm-include-order -header-filter=.* %s \
+// RUN:   -- -isystem %S/Inputs/Headers -I %S/Inputs/overlapping | \
+// RUN:   grep "note: this fix will not be applied because it overlaps with another fix"
+
+#include <s.h>
+#include "o.h"
+
+// Test that clang-tidy takes into account in which file we are doing the
+// replacements to determine if they overlap or not. In the file "o.h" there is
+// a similar error at the same file offset, but they do not overlap.