diff --git a/codepy/toolchain.py b/codepy/toolchain.py
index 0211b5c..7f8ccb9 100644
--- a/codepy/toolchain.py
+++ b/codepy/toolchain.py
@@ -168,6 +168,8 @@ def get_dependencies(self, source_files):
             raise CompileError(f"getting dependencies failed: {stderr}")
 
         lines = join_continued_lines(stdout.split("\n"))
+        lines = [line for line in lines
+                 if not (line.strip() and line.strip()[0] == "#")]
         from pytools import flatten
         return set(flatten(
             line.split()[2:] for line in lines))