diff --git a/clang-tools-extra/include-cleaner/lib/Analysis.cpp b/clang-tools-extra/include-cleaner/lib/Analysis.cpp
--- a/clang-tools-extra/include-cleaner/lib/Analysis.cpp
+++ b/clang-tools-extra/include-cleaner/lib/Analysis.cpp
@@ -28,10 +28,29 @@
 #include "llvm/ADT/StringSet.h"
 #include "llvm/Support/Error.h"
 #include "llvm/Support/ErrorHandling.h"
+#include <cassert>
 #include <string>
 
 namespace clang::include_cleaner {
 
+namespace {
+bool shouldIgnoreMacroReference(const Macro &M) {
+  static const auto *MacroNamesToIgnore = new llvm::StringSet<>{
+      // C standard says these are implementation defined macros, hence most of
+      // the standard library providers implement it by defining these as macros
+      // that resolve to themselves.
+      // This results in surprising behavior from users point of view (we
+      // generate a usage of stdio.h, in places unrelated to standard library).
+      // FIXME: Also eliminate the false negatives by treating declarations
+      // resulting from these expansions as used.
+      "stdin",
+      "stdout",
+      "stderr",
+  };
+  return MacroNamesToIgnore->contains(M.Name->getName());
+}
+} // namespace
+
 void walkUsed(llvm::ArrayRef<Decl *> ASTRoots,
               llvm::ArrayRef<SymbolReference> MacroRefs,
               const PragmaIncludes *PI, const SourceManager &SM,
@@ -51,7 +70,8 @@
   }
   for (const SymbolReference &MacroRef : MacroRefs) {
     assert(MacroRef.Target.kind() == Symbol::Macro);
-    if (!SM.isWrittenInMainFile(SM.getSpellingLoc(MacroRef.RefLocation)))
+    if (!SM.isWrittenInMainFile(SM.getSpellingLoc(MacroRef.RefLocation)) ||
+        shouldIgnoreMacroReference(MacroRef.Target.macro()))
       continue;
     CB(MacroRef, headersForSymbol(MacroRef.Target, SM, PI));
   }
diff --git a/clang-tools-extra/include-cleaner/unittests/AnalysisTest.cpp b/clang-tools-extra/include-cleaner/unittests/AnalysisTest.cpp
--- a/clang-tools-extra/include-cleaner/unittests/AnalysisTest.cpp
+++ b/clang-tools-extra/include-cleaner/unittests/AnalysisTest.cpp
@@ -483,5 +483,29 @@
                 Pair(Code.point("partial"), UnorderedElementsAre(Partial)))));
 }
 
+TEST_F(WalkUsedTest, IgnoresIdentityMacros) {
+  llvm::Annotations Code(R"cpp(
+  #include "header.h"
+  void $bar^bar() {
+    $stdin^stdin();
+  }
+  )cpp");
+  Inputs.Code = Code.code();
+  Inputs.ExtraFiles["header.h"] = guard(R"cpp(
+  #include "inner.h"
+  void stdin();
+  )cpp");
+  Inputs.ExtraFiles["inner.h"] = guard(R"cpp(
+  #define stdin stdin
+  )cpp");
+
+  TestAST AST(Inputs);
+  auto &SM = AST.sourceManager();
+  auto MainFile = Header(SM.getFileEntryForID(SM.getMainFileID()));
+  EXPECT_THAT(offsetToProviders(AST, SM),
+              UnorderedElementsAre(
+                  // FIXME: we should have a reference from stdin to header.h
+                  Pair(Code.point("bar"), UnorderedElementsAre(MainFile))));
+}
 } // namespace
 } // namespace clang::include_cleaner