Auto Focus Not Working

I had a same problem, Auto Focus works in all the Basic modes but it did not work in Advanced and Manual modes.  After couple of hours of frustration I found the solution. It worked for me, I hope it will work for you too.
Follow step by step instructions. Start the Camera
Go to M (Manual Mode) Press Menu Button Go to 6-th Tab Custom Functions (C.Fn) Select Clear settings Select Clear all Custom Func. (C.Fn)
This should fix your problem
Go back to shooting more and try your Auto Focus

There are several possibilities. Start with these first 2 steps:

1) If you have more than one lens, try a different lens. If the problem persists with different lenses, then the problem is in the camera. If the problem goes away with a different lens, then the problem is in the lens.

2) Clean the contacts between the lens and camera. Gently rub the contacts with a clean pencil eraser, and hold the item with the contacts facing down so that the eraser debris falls onto the table, not into the lens or camera.

If this doesn't fix the problem then it is internal - either in the lens or camera. Refer to step 1 to test to see which it is. Then you need to send the appropriate item into Canon for cleaning and repair. Canon may request that you send both the camera and lens, so call them before you send the item in for repair.