diff --git a/waflib/Context.py b/waflib/Context.py
index 87c71117..a9e3a663 100644
--- a/waflib/Context.py
+++ b/waflib/Context.py
@@ -331,14 +331,15 @@ class Context(ctx):
 		if Logs.verbose and not kw['shell'] and not Utils.check_exe(cmd[0]):
 			raise Errors.WafError('Program %s not found!' % cmd[0])
 
-		wargs = {}
+		cargs = {}
 		if 'timeout' in kw:
 			if kw['timeout'] is not None:
-				wargs['timeout'] = kw['timeout']
+				if kw['shell']:
+					Logs.warn('Shell commands cannot timeout %r', cmd)
 			del kw['timeout']
 		if 'input' in kw:
 			if kw['input']:
-				wargs['input'] = kw['input']
+				cargs['input'] = kw['input']
 				kw['stdin'] = subprocess.PIPE
 			del kw['input']
 
@@ -347,7 +348,7 @@ class Context(ctx):
 				kw['cwd'] = kw['cwd'].abspath()
 
 		try:
-			ret, out, err = Utils.run_process(cmd, kw, wargs)
+			ret, out, err = Utils.run_process(cmd, kw, cargs)
 		except Exception as e:
 			raise Errors.WafError('Execution failure: %s' % str(e), ex=e)
 
@@ -415,14 +416,15 @@ class Context(ctx):
 		if quiet is None:
 			self.to_log(cmd)
 
-		wargs = {}
+		cargs = {}
 		if 'timeout' in kw:
 			if kw['timeout'] is not None:
-				wargs['timeout'] = kw['timeout']
+				if kw['shell']:
+					Logs.warn('Shell commands cannot timeout %r', cmd)
 			del kw['timeout']
 		if 'input' in kw:
 			if kw['input']:
-				wargs['input'] = kw['input']
+				cargs['input'] = kw['input']
 				kw['stdin'] = subprocess.PIPE
 			del kw['input']
 
@@ -431,7 +433,7 @@ class Context(ctx):
 				kw['cwd'] = kw['cwd'].abspath()
 
 		try:
-			ret, out, err = Utils.run_process(cmd, kw, wargs)
+			ret, out, err = Utils.run_process(cmd, kw, cargs)
 		except Exception as e:
 			raise Errors.WafError('Execution failure: %s' % str(e), ex=e)
 
diff --git a/waflib/Utils.py b/waflib/Utils.py
index f99dae23..9e84109d 100644
--- a/waflib/Utils.py
+++ b/waflib/Utils.py
@@ -866,15 +866,17 @@ def run_regular_process(cmd, kwargs, cargs={}):
 			out, err = proc.communicate(**cargs)
 		except TimeoutExpired:
 			proc.kill()
-			out, err = proc.communicate(**cargs)
+			out, err = proc.communicate()
+			raise TimeoutExpired(proc.args, timeout=cargs['timeout'], output=out, stderr=err)
 		status = proc.returncode
 	else:
 		out, err = (None, None)
 		try:
 			status = proc.wait(**cargs)
-		except TimeoutExpired:
+		except TimeoutExpired as e:
 			proc.kill()
-			status = proc.wait(**cargs)
+			proc.wait()
+			raise e
 	return status, out, err
 
 def run_process(cmd, kwargs, cargs={}):
diff --git a/waflib/processor.py b/waflib/processor.py
index 01fb70f5..b1ce9ac6 100755
--- a/waflib/processor.py
+++ b/waflib/processor.py
@@ -35,7 +35,8 @@ def run():
 			out, err = proc.communicate(**cargs)
 		except TimeoutExpired:
 			proc.kill()
-			out, err = proc.communicate(**cargs)
+			out, err = proc.communicate()
+			raise TimeoutExpired(proc.args, timeout=cargs['timeout'], output=out, stderr=err)
 		ret = proc.returncode
 	except Exception as e:
 		exc_type, exc_value, tb = sys.exc_info()