If you enlist you usually have to go to MEPS (Military Enterance Processing Station), and that's where you do your initial physical/shots to get into the military. I'm not sure if new officers have to do this or not.
http://usmilitary.about.com/od/joiningthemilitary/a/mepsglance.htm
Same with officers.
First you fill out your packet (this is oldhat to you, koojo, but thought I'd throw it in for folks not far along). When they look over your packet, they might see medical stuff they don't like. Unless it's a permanent disqualification (one arm, etc.), they'll put through a waiver to go to MEPS. This takes a few weeks, but is pretty rubber stamp.
After you get the waiver, you go to MEPS. You do exactly the same MEPS as all the enlisted (with the exception of the ASVAB, which you do not take). So you can look online about what to expect at your day at MEPS. About.com had a very good guide.
You will see a doctor who will look over what you were wiavered for and if possible will analyze you for it. I had an old broken bone that I needed waivered. He examined it and said it was fine. I also had an old history of heartburn, which he couldn't examine and wouldn't say was fine, so I was disqualified. This is normal for folks who had conditions they needed waivered.
Then, depending on the condition, you will either disqualified and referred to a specialist (like for allergies and whatnot) or are just disqualified. If you go to a specialist, they either okay you, or disqualify you. In the event you are disqualified, your recruiter will put through for another waiver (the first was to get you to MEPS, the second was to get a final "okay"). If you get denied again, you can appeal, but it's an uphill battle that may not end well. If you get the waiver, you are done with the process, do not have to return to MEPS and go to the state and fed rec boards.
Hope this helps someone...