You don't use the crate as punishment, do you? Has he had any rewards for being in the crate? How long is he usually crated when you can get him in there? I think what you need to do is make crating a positive experience for the dog, first of all, and that'll help him relax in there.
If he's pretty frightened of it, try putting his food in the crate, way at the back so he has to go in to eat. Just leave the crate door open and don't offer him food or water anywhere else.
Also.. What kind of crate are you using? Do you have a plastic airline-style crate, or a wire crate? If you have the plastic crate, try the wire one. If you have the wire crate, try a plastic one. Sometimes dogs feel more comfortable in one kind of crate than the other.
Or, like Saje said, he might just not feel secure enough in the crate. In that case, try an expen (if he's small) or a puppy-proofed room to keep him confined.