It could quite possibly be separation anxiety.
What does he do when he wakes? Are his eyes still closed or are they wide open and darting around the room? Does the crying continue over several minutes, or is it a loud cry, then a sort of break, then another one? Are there any tears? Does he stop when you enter the room? When you go to him, what do you do? Do you turn on a light?
The reason I ask is that it could also be a mantra cry. Mine lately has been doing that...she'll let out a loud cry after being asleep for an hour, then break, then do another one, then it ends for the rest of the night. It's really strange. It could last maybe 30 seconds, but she never seems to be awake. There are no tears. It doesn't happen every night, maybe every few nights. She'll even lift her head and seem to look around, but her eyes are closed.
If it is separation anxiety, you could try doing wake to sleep then and see if it works. Or you could observe for a few nights and see if he's really awake (you'll see tears), or if you're doing something to wake him when he's really asleep. I swear, this whole mantra cry business is soo confusing. They really *sound* awake. Often what happens is mom or dad goes into the room when they hear this cry, turn on a bright light or do something to wake them up fully.
At his age though, there's a really good chance it could be separation anxiety. Spend a few nights observing; go in before he normally wakes and see if you can prevent it by gently laying a hand on his back or tummy before he wakes fully (when he stirs). Don't say anything, keep the room dark. That's the naptime version of wake to sleep, but it can certainly work for night sleep.
Hope this helps!
*HUGS*
Sonya =P