Shaking problem

I noticed whenever I hold my cat sometimes he shakes. It will stop for a second and then start again. It is not all the time but when he shakes he shakes for a couple seconds then it stops for a second then he shakes for a couple seconds then it stops for a second and so on.

You mean like shivering?  Is it his entire body?  Not sure what that is.  I had a cat that would do that on a rare occasion when she was sleeping, and our Vet checked her out and never found anything, and figured she  might be having dreams.  But your cat is not sleeping when this happens, so it might be worth checking out with your Vet.