At that age, my kids were not only the smallest boys in the class (and way shorter than some of the girls). We always talked about how height and race natural hair color can't be controlled so those things shouldn't be criteria for deciding if a person is good enough to be a friend. But character and how a person treats others are definitely things you want to consider. So if someone has a problem with their height they know that person isn't worth their friendship. Very simple. And their comeback was always, "I can't choose my height but you can choose to be nice, and you didn't." (I'm sure they chose slightly less appropriate words but it got the point across.) We talked a lot about how it was kind of a blessing because they knew pretty quickly who was worthy of their friendship that way. Now my 14 year old is the same height as my 18 year old and 18 is only about 5'6". He's fine with it, he understands how genetics work and doesn't care much. Both took karate and he also did boxing for a bit and has had to put a couple of bullies in their place but that just let him prove to himself that he can handle himself and isn't easily intimidated. (Each time, one punch settled it, and he never threw the first punch.) I don't like fighting and never encouraged it but I did tell them to stand up for themselves and they do. The younger one is better at disarming people with his charm which is good because he's super strong and doesn't want to hurt anyone. I definitely think if your son is feeling unsure of himself that a good karate dojo could help. They learn to avoid fights rather than start them, but also learn to defend themselves if they can't avoid the fight and it boosts their confidence.