This might be an odd suggestion, but do you know if he refuses to use the toilet because he's afraid of it? I know that small children sometimes tell stories about monsters (snakes/rats) coming up out of a toilet. And if you stop to think about it, toilets might be dangerous--the stuff in them goes away mysteriously, with a certain amount of noise; maybe they could eat small people too. :)

Might it help to go over the mechanics/plumbing of a toilet and how it works with him? Possibly simplified--I donno how good he is with models/conceptual information.