diff --git a/Makefile b/Makefile
index 39812d5ca99..03ffb2ad788 100644
--- a/Makefile
+++ b/Makefile
@@ -4,7 +4,8 @@ all:
 	python setup.py build_ext --inplace
 
 clean:
-	find . -name "*.so" -o -name "*.pyc" -o -name "*.pyx.md5" -o -name "*.c" -o -name "*.pyd" | xargs rm -f
+	find . -name "*.so" -o -name "*.pyc" -o -name "*.pyx.md5" -o -name "*.pyd" | xargs rm -f
+	find . -name "*.pyx" -exec ./tools/rm_pyx_c_file.sh {} \;
 
 test:
 	python -c "import skimage, sys, io; sys.exit(skimage.test_verbose())"
diff --git a/tools/rm_pyx_c_file.sh b/tools/rm_pyx_c_file.sh
new file mode 100755
index 00000000000..1febb19e35b
--- /dev/null
+++ b/tools/rm_pyx_c_file.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+# Accepts a .pyx file path and deletes an associated .c file, if present.
+filename="${1%.*}".c
+if [ -e "$filename" ]; then
+	rm -f "$filename";
+fi