I have recently inherited the maintanence of a website. It was designed using html frames a very long time ago. So the header is frame, side bar a frame and main content section a frame. It gets very few hits from search engines. I am suprised that it doesn't show up in many search queries. All the pages on the site are indexed by all the major search engines.
It does have a low page rank and I am working on that.

But my question is do search engines penalise your site for using frames?
Or am I missing something else?