We had the same issue, and I finally realized that she had trouble rolling from her front to her back in her crib, even though she could do it on the floor. So, we would just turn her over and she'd go right back to sleep, that way we weren't up for a long time as well as her, since she'd stop crying right away. At like 8 1/2 months, she started doing it on her own, and we didn't have to turn her over anymore. She still wakes up sometimes at like 3 or so, and I think she just feels the anxiety of being alone and wondering where we are, she starts crying. We hold her and comfort her for a couple of minutes, and then she's fine back in her crib again. I figure she's only going to be this age once, and it's so important to teach her we love her, to trust us, and feel comfortable with the world around her. So, as sleep deprived as I am, the trade off is worth it to me to give her a secure beginning. If it was effecting me more, it would be a different story, but just waking up once for a short while seems like no big deal. I can deal with losing sleep for a couple of years, she would be forever affected if her cries are not answered. Just give it time, it will eventually stop, especially since he's such a good sleeper in general. And, when you have to wake up at 3 am, look down and treasure the moment, it will be quickly fleeting, and at some point he won't want to be bothered with you.