How long have you had him for? If you have recently adopted him, he could have the cat flu, perhaps you might want to take him back to the shelter or vet and see if you have caught it early. It could be just an allergy, but in kittens it is better to find out sooner rather than later. When we adopted Jazzy, she was sneezing a day after we brought her home, we took her back and were able to get free medication for up to about 4 weeks after the adoption. Usually if the kittens are sick they keep them medicated and cleared up before they go up for sale, but there are some cases where the signs are missed. Keep an eye out for runny nose, lots of sneezing, breathing through the mouth (due to blocked sinuses) and oozing tear ducts.
I suggest you take him JUST in case. It may be nothing. but as i said, better to find out sooner than later.