There are extensions for firefox that allow you to do this in the browser if you only want to check a few pages.
One is the "Unused selectors" in Pagespeed, which is an extension to firebug. Two others are "Css Usage" (another extension to firebug which allows you to export the "cleaned" css file) and "Dustme selectors" which is a separate extension for firefox. The development of the last two has been a bit fragmented, and all three can produce "false negatives" so I'd use with care - but may be a place to start.
Edit Just noticed the exact question was
what elements are not being used in the CSS file?
The suggested tools will identify unused css rules, which is usually the goal when trying to clean up css. But it is different from identifying HTML elements that haven't been "used" in the css. Are you sure that's what is wanted?