He's only 11 weeks old, it could be his testicles, they may not have descended into the scrotum yet. In some puppies they actually go up and down for a while before they decide to stay in the scrotum. Next time he goes for shots have the vet take a look. If they're testicles they'll be about the size of medium grapes.
Ghilly
Are these at the base area of his penis/sheath? You might be seeing the bulbous glands that can enlarge when the make gets excited, needs to pee, etc. do a Google search for photos of bulbous gland in make dogs and see if that is what you may be seeing. If so, very normal.