Index: lib/Analysis/IPA/CallGraphSCCPass.cpp
===================================================================
--- lib/Analysis/IPA/CallGraphSCCPass.cpp
+++ lib/Analysis/IPA/CallGraphSCCPass.cpp
@@ -243,7 +243,14 @@
       
       assert(!CallSites.count(I->first) &&
              "Call site occurs in node multiple times");
-      CallSites.insert(std::make_pair(I->first, I->second));
+      
+      CallSite CS(I->first);
+      if (CS) {
+        Function *Callee = CS.getCalledFunction();
+        // Ignore intrinsics because they're not really function calls.
+        if (!Callee || !(Callee->isIntrinsic()))
+          CallSites.insert(std::make_pair(I->first, I->second));
+      }
       ++I;
     }
     
Index: test/Transforms/InstCombine/no_cgscc_assert.ll
===================================================================
--- test/Transforms/InstCombine/no_cgscc_assert.ll
+++ test/Transforms/InstCombine/no_cgscc_assert.ll
@@ -0,0 +1,19 @@
+; RUN: opt < %s -inline -instcombine -S | FileCheck %s
+
+; PR21403: http://llvm.org/bugs/show_bug.cgi?id=21403
+; When the call to sqrtf is replaced by an intrinsic call to fabs,
+; it should not cause a problem in CGSCC. 
+
+define float @bar(float %f) #0 {
+  %mul = fmul fast float %f, %f
+  %call1 = call float @sqrtf(float %mul) #0
+  ret float %call1
+
+; CHECK-LABEL: @bar(
+; CHECK-NEXT: call float @llvm.fabs.f32
+; CHECK-NEXT: ret float
+}
+
+declare float @sqrtf(float) #0
+
+attributes #0 = { readnone "unsafe-fp-math"="true" }