In a recent interview while promoting the upcoming third season of The Walking Dead, actor Norman Reedus also mentioned that he was meeting with director Troy Duffy and the other half of the Boondock Saints, Sean Patrick Flanery, about a third film in the series:
“I’m in L.A right now,” Reedus said when asked about a third “Boondock Saints” movie. “I’m meeting with Sean [Patrick Flanery] and Troy [Duffy] tonight. I just landed a couple hours ago and tonight I’m going over to Troy’s house with Sean. It’s definitely in the works. Look for it. It’s gonna be crazy.”
After writer-director Troy Duffy's ego trip while making The Boondock Saints in 1999, which became the subject of the 2003 documentary Overnight, caused him to alienate friends, relatives and business partners as well as practically end his filmmaking career just as it was beginning it was a shock to everyone when he returned 10 years later for his second film, 'The Boondock Saints II: All Saints Day'.
While All Saints Day was not met as favourably as the first film it may have done enough to spark interest in making a third film if what Norman Reedus said is true, whether there is a script or any studio involvement is as of yet unknown.

Source
The Boondock Saints are my fave series of movies.
Got to love any movie where some dude gets killed by having a toilet dropped on his head!