Filmography
| Year | Film | Role | Notes |
|---|---|---|---|
| 1985 | Explorers | Ben Crandall | |
| 1988 | Lion's Den | Unnamed | |
| 1989 | Dead Poets Society | Todd Anderson | |
| 1989 | Dad | Billy Tremont | |
| 1991 | White Fang | Jack Conroy | |
| 1991 | Mystery Date | Tom McHugh | |
| 1992 | Waterland | Mathew Price | |
| 1992 | A Midnight Clear | Will Knott | |
| 1993 | Rich in Love | Wayne Frobiness | |
| 1993 | Alive | Nando Parrado | |
| 1994 | Reality Bites | Troy Dyer | Nominated — MTV Movie Award for Best Kiss (Shared nomination with Winona Ryder) |
| 1994 | White Fang 2: Myth of the White Wolf | Jack Conroy (uncredited) | |
| 1994 | Quiz Show | Don Quixote Student (uncredited) | |
| 1994 | Floundering | Jimmy | |
| 1995 | Before Sunrise | Jesse Wallace | Nominated — MTV Movie Award for Best Kiss (Shared nomination with Julie Delpy) |
| 1995 | Search and Destroy | Roger | |
| 1997 | Gattaca | Vincent Anton Freeman / Jerome Morrow | |
| 1998 | Great Expectations | Finnegan 'Finn' Bell | |
| 1998 | The Newton Boys | Jess Newton | |
| 1999 | The Velocity of Gary | Nat | |
| 1999 | Joe the King | Len Coles | |
| 1999 | Snow Falling on Cedars | Ishmael Chambers | |
| 2000 | Hamlet | Hamlet | |
| 2001 | Waking Life | Jesse Wallace | |
| 2001 | Tape | Vince | |
| 2001 | Training Day | Jake Hoyt |
|
| 2002 | Chelsea Walls | Sam (voice) (uncredited) | |
| 2002 | The Jimmy Show | Ray | |
| 2003 | Alias | CIA Agent James L. Lennox | Episode: "Double Agent" |
| 2004 | Taking Lives | James Costa / Martin Asher | |
| 2004 | Before Sunset | Jesse Wallace |
|
| 2005 | Assault on Precinct 13 | Sergeant Jake Roenick | |
| 2005 | Lord of War | Agent Jack Valentine | |
| 2006 | One Last Thing... | Earl Jameison (uncredited) | |
| 2006 | The Hottest State | Vince | |
| 2006 | Fast Food Nation | Pete | |
| 2007 | Before the Devil Knows You're Dead | Hank Hanson | Gotham Award for Best Ensemble Cast |
| 2008 | What Doesn't Kill You | Paulie McDougan | |
| 2008 | Chelsea on the Rocks | Himself | Documentary |
| 2009 | New York, I Love You | Writer | |
| 2009 | Staten Island | Sully Halverson | |
| 2009 | Corso: The Last Beat | Narrator / Himself | Documentary |
| 2009 | Daybreakers | Edward Dalton | |
| 2010 | Brooklyn's Finest | Detective Salvatore "Sal" Procida | |
| 2011 | Moby Dick | Starbuck | TV miniseries |
| 2011 | The Woman in the Fifth | Tom Ricks | |
| 2012 | Sinister | Ellison Oswalt | |
| 2013 | Getaway | Brent Magna | post-production |
| 2013 | Before Midnight | Jesse Wallace | post-production |
| TBD | Boyhood | Dad | filming |
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