Index: llvm/trunk/lib/Fuzzer/FuzzerInternal.h
===================================================================
--- llvm/trunk/lib/Fuzzer/FuzzerInternal.h
+++ llvm/trunk/lib/Fuzzer/FuzzerInternal.h
@@ -147,6 +147,7 @@
   uint8_t *CurrentUnitData = nullptr;
   std::atomic<size_t> CurrentUnitSize;
   uint8_t BaseSha1[kSHA1NumBytes];  // Checksum of the base unit.
+  bool RunningCB = false;
 
   size_t TotalNumberOfRuns = 0;
   size_t NumberOfNewUnitsAdded = 0;
Index: llvm/trunk/lib/Fuzzer/FuzzerLoop.cpp
===================================================================
--- llvm/trunk/lib/Fuzzer/FuzzerLoop.cpp
+++ llvm/trunk/lib/Fuzzer/FuzzerLoop.cpp
@@ -286,7 +286,7 @@
 void Fuzzer::AlarmCallback() {
   assert(Options.UnitTimeoutSec > 0);
   if (!InFuzzingThread()) return;
-  if (!CurrentUnitSize)
+  if (!RunningCB)
     return; // We have not started running units yet.
   size_t Seconds =
       duration_cast<seconds>(system_clock::now() - UnitStartTime).count();
@@ -532,7 +532,9 @@
   UnitStartTime = system_clock::now();
   ResetCounters();  // Reset coverage right before the callback.
   TPC.ResetMaps();
+  RunningCB = true;
   int Res = CB(DataCopy, Size);
+  RunningCB = false;
   UnitStopTime = system_clock::now();
   (void)Res;
   assert(Res == 0);
Index: llvm/trunk/lib/Fuzzer/test/CMakeLists.txt
===================================================================
--- llvm/trunk/lib/Fuzzer/test/CMakeLists.txt
+++ llvm/trunk/lib/Fuzzer/test/CMakeLists.txt
@@ -109,6 +109,7 @@
   ThreadedLeakTest
   ThreadedTest
   TimeoutTest
+  TimeoutEmptyTest
   TraceMallocTest
   )
 
Index: llvm/trunk/lib/Fuzzer/test/TimeoutEmptyTest.cpp
===================================================================
--- llvm/trunk/lib/Fuzzer/test/TimeoutEmptyTest.cpp
+++ llvm/trunk/lib/Fuzzer/test/TimeoutEmptyTest.cpp
@@ -0,0 +1,14 @@
+// This file is distributed under the University of Illinois Open Source
+// License. See LICENSE.TXT for details.
+
+// Simple test for a fuzzer. The fuzzer must find the empty string.
+#include <cstdint>
+#include <cstddef>
+
+extern "C" int LLVMFuzzerTestOneInput(const uint8_t *Data, size_t Size) {
+  static volatile int Zero = 0;
+  if (!Size)
+    while(!Zero)
+      ;
+  return 0;
+}
Index: llvm/trunk/lib/Fuzzer/test/fuzzer-timeout.test
===================================================================
--- llvm/trunk/lib/Fuzzer/test/fuzzer-timeout.test
+++ llvm/trunk/lib/Fuzzer/test/fuzzer-timeout.test
@@ -12,3 +12,8 @@
 SingleInputTimeoutTest-NOT: Test unit written to ./timeout-
 
 RUN: LLVMFuzzer-TimeoutTest -timeout=1 -timeout_exitcode=0
+
+RUN: not LLVMFuzzer-TimeoutEmptyTest -timeout=1 2>&1 | FileCheck %s --check-prefix=TimeoutEmptyTest
+TimeoutEmptyTest: ALARM: working on the last Unit for
+TimeoutEmptyTest: == ERROR: libFuzzer: timeout after
+TimeoutEmptyTest: SUMMARY: libFuzzer: timeout