I purchased a D90 body few weeks ago and then bought a 85mm f/1.8 D lens. I mounted it on and started clicking a few pictures. Auto-Focus didn't work. I quickly checked the AF/MF switch on the body. It was set to AF. I re-checked the software settings for auto-focus (a) and it all looked perfect. I got a little worked up and did a quick google search and figured that some people had to even return and get a replacement for their body for this reason. Read a little further and figured that mounting has to be perfect, the lens has to rotated till the exact last lock-click.

So basically, you might encounter this problem if you are changing lens or you bought lens and body separately and fixed the lens yourself. The fix is to make sure you mount to absolute perfection without being too hard at it. If Auto-Focus does not work try gently screwing it a little further. It should work. If you still face issues, I recommend you to head to a Nikon Service Centre and have someone do it for you.

Happy Clicking!