Tom Noonan
- Wonderstruck
2017 Walter
- Anomalisa
2015 Everyone Else (voice)
- Late Phases
2014 Father Roger Smith
- The Shape of Something Squashed
2014 Director
- Stoney
2010 Charles Stoney
- The House of the Devil
2009 Mr. Ulman
- Where the Wild Things Are
2009 Thanks
- Synecdoche, New York
2008 Sammy Barnathan
- The Alphabet Killer
2008 Ray Gullikson
- Seraphim Falls
2007 Minister Abraham
- Snow Angels
2007 Mr. Chervenick
- June Weddings
2007 RJ
- Ice Cream Ants
2006 The Thinker
- The Roost
2005 The Horror Host
- They're Made Out of Meat
2005 Duncan
- A Buck's Worth
2005
- Hair High
2004 Principal (voice)
- Madness and Genius
2003 Frank Donovan
- Eight Legged Freaks
2002 Joshua Taft (uncredited)
- The Pledge
2001 Gary Jackson
- Knockaround Guys
2001 Sheriff Decker
- Inside 'Manhunter'
2001 Himself
- Bullet in the Brain
2001 Anders
- An Unpredictable Thing
2001 Writer
- The Photographer
2000 Butler
- The Opportunists
2000 Mort Stein
- The Astronaut's Wife
1999 Jackson McLaren
- Wang Dang
1999 Director
- Phoenix
1998 Chicago
- The Wife
1996 Director
- Heat
1995 Kelso
- The Pesky Suitor
1995 Editor
- What Happened Was...
1994 Director
- Last Action Hero
1993 Ripper / Tommy Noonan
- The 10 Million Dollar Getaway
1991 Mr. Y
- Bone Daddy
1991 Director
- Red Wind
1991 Writer
- RoboCop 2
1990 Cain
- Collision Course
1989 Scully
- Mystery Train
1989 Man in Diner
- The Monster Squad
1987 Frankenstein
- Manhunter
1986 Francis Dollarhyde
- F/X
1986 Varrick
- The Man with One Red Shoe
1985 Reese
- Tom Goes to the Bar
1985 Tom
- Best Defense
1984 Holtzman
- Easy Money
1983 Paddy
- Eddie Macon's Run
1983 Darryl Potts
- Wolfen
1981 Ferguson
- Heaven's Gate
1980 Jake
- Gloria
1980 2nd Man / Gangster
- Rage!
1980 Bo
- Willie & Phil
1980 Man In Park
