Thread necromancy fail. I am not sure if this was true in the past but I think most of the posters in this thread are incorrect. The way to eradicate an enemy religion is to specifically capture their holy city, then go use an Inquisitor on it to "remove heresy". This kills the holy city ability of that city, however it won't remove the religion fully from the game until you go and convert other cities following that religion. However, yes, using an inquisitor wipes that religion out of that holy city. It would only come back if it's surrounded by other cities following that religion. Besides blocking enemy prophets, this is the main purpose of the inquisitor. Perhaps in old patches it was bugged or something, but reading the first page of this thread made me go... UMM wtf game are you playing? I routinely do this in my games to make my religion the dominant one... go take the enemy holy cities and remove heresy.