The title of the film and the novel it's based on is taken from the song "Breakfast on Pluto" by Don Partridge. The song is used as part of the soundtrack and Liam Cunningham quotes a few lines (including the title) from the lyrics.
The school master in whose class Patrick "Kitten" Braden is writing the essay about his conception as he imagines it is played by the author of the source novel and co-writer of the screenplay Pat McCabe.
Both Neil Jordan and Cillian Murphy described the filming location for the caravan in the quarry (a quarry near Larne in Northern Ireland) as a rather sinister place. There were rumors that many dead bodies were buried there.
One of the IRA men threatening to kill Patrick "Kitten" Braden, the one he/she calls Mr. Killing Man, is played by Eamonn Owens who made his film debut in another Neil Jordan film, The Butcher Boy (1997) where he played the title character.
The scenes where Patrick "Kitten" Braden goes to see his mother were filmed in Northern Ireland. While they were shooting, a RUC helicopter was persistently staying in the air above them. Neil Jordan joked they were keeping a close eye on him, because this was the the guy who made Michael Collins (1996) shooting a film in Northern Ireland.
While they don't have any scenes together, and his is more of a cameo, Ruth Negga and Dominic Cooper also appear together in the critically acclaimed AMC television show "Preacher." They have also been dating since 2010.