If you are using CSS it is more than likely due to the "box model" problem with IE. Google it and you will get tons of info on what to do about it. If that's not it let me know and we'll figure it out.
I had the same problem a few weeks back. IE have a very mad issue of not following the basic rules set for web browsers. But hey its the leading browser so we got to make our sites compatible! I would suggest doing a google search for CSS fixes for IE. That is how I found many solutions. If I can get a link I will post it.