It was confirmed in New Vegas when Bruce Isaac told the Courier that the Chosen One did indeed have a son, and that his son was the reason why he ran away and is currently hiding in Novac.
Joshua Sawyer has already confirmed it as canon through his FormSpring. However, I can't find his response, (That was a long time ago.) so I will just have to stick with my first point until Sawyer responds to this question again. Skål! 01:22, August 27, 2012 (UTC)
Hello AnimeandCartoonFreak, you've been banned from Nukapedia chat for a period of 3 days for violating the following rules of chat: Trolling or general irritation or disruption of other users. You should take this opportunity to completely familiarize yourself with Nukapedia'schat policies, if you have not yet done so.