Several small snippets were taken out by Sam Mendes to maintain the narrative flow of the film; these scenes are availible on the DVD:
After the Sullivans eat dinner, Annie and Michael Sr. clean dishes at the sink. Annie cuts her finger and Michael bandages it for her.
At McGovern's wake, Rooney greets Annie, and Michael Sr. notices Michael Jr. limping and remarks that he needs new shoes. Annie goes into the kitchen with all of the other gangsters' wives while Michael Sr. offers his condolences to Finn, whose chilly reception implies that McGovern's death was a hit.
An extended version of Mr. Rooney and the Sullivan boys' dice game in the wine cellar; Michael takes the dice out of his shoe (his reason for limping) and we intercut between the dice game and Annie drinking in the kitchen.
An extended version of Michael Jr.'s encounter with Connor, where Michael Jr. spies on a couple preparing to have sex.
Rooney drinks with Michael Sr. before delivering McGovern's eulogy, making sure that Finn hasn't caused any trouble. Connor comes downstairs and Rooney chastizes him for not showing more respect. Rooney gets up and Connor comments that he never expected McGovern's wake would have so many mourners, then tells Michael Sr. "yours would."
After Michael Jr. witnesses Finn's murder, he sneaks back into bed just before Annie comes to tuck him in. He lays awake staring out the window at the garage, where Michael Sr. scrubs his hands and puts his machine gun away.
A long, tracking shot of the nightclub where Michael Sr. is set up to be killed, showing a pool hall, casino, speakeasy, jazz club, and brothel to be contained within the establishment. This scene also includes a longer version of the bouncer's speech to Michael about his job.
The morning after Michael Sr. shoots the banker, he and Michael Jr. go to church; Michael Sr. lights a candle for the banker's soul and then goes to confession.
Michael Jr. prepares to go to bed in the motor lodge while Michael Sr. cleans his son's clothes. Michael Jr. gets upset because his father tells him that he's going to leave him at Sara's until Connor is dead. After Michael Jr. gets into bed he says that he's cold and forgot a sweater, so Michael Sr. gives him his.
Maguire goes through the Sullivan's home during Annie and Peter's wake. He looks through Michael Sr.'s closet, is amused by the presence of Catholic icons (it's implied Maguire's an atheist), and finally searches the boys' room. He steals Michael Jr.'s tobacco (stolen during the opening credits), then uncovers two toy guns hidden in a dresser drawer, prompting Maguire to get out his camera and photograph them.
After Michael Jr. asks his father for a cut of the money, he goes to the bathroom. The diner waitress, a dead ringer for Annie (played by Jennifer Jason Leigh's sister) tries to flirt with Michael Sr. and asks him to dance, but he turns her down.
The infamous deleted Al Capone sequence, where he yells at Rooney for having to take care of Connor, and then snaps when he thinks Maguire is looking at him cockeyed, prompting a temper tantrum.
Michael Jr. feeds his wounded father soup. After Michael Sr. falls asleep, the son then gets out the father's revolver and play-acts killing someone in the mirror.