Duchovny caused controversy when it became public that he was the primary reason that filming of The X-Files series was moved from Vancouver, British Columbia to Los Angeles in 1998. Many residents of Vancouver were upset with Duchovny over scripted jokes on Conan O'Brien's late night show about the city's heavy rainfall; he joked that "Vancouver is a very nice place, if you like 400 inches of rainfall a day." He also stated, "Of course, I'm tired of the rain. But if I wasn't married to a woman that lives in L.A. I'd stay in Vancouver. It's a lovely city. During the run of The X-Files, he also made several guest appearances in the cult TV satire The Larry Sanders Show, playing himself, but adding a strong attraction to Sanders. In the final episode of the series, he performed a parody of Sharon Stone's 'flashing' scene from Basic Instinct.
Duchovny has guest hosted Saturday Night Live twice (May 13, 1995 and May 9, 1998). Both shows were season finales. In 2000, he starred in the feature film Return to Me, a romantic comedy/drama. Return to Me was directed by Bonnie Hunt and co-starred Minnie Driver and Carroll O'Connor. In 2001, Duchovny played a hand model in the Ben Stiller comedy, Zoolander. He also played the role of Ira Kane in the movie Evolution along side Seann William Scott that same year.
He also appeared in a celebrity edition of Who Wants to Be a Millionaire? in May 2000. He got up to $250,000, but answered his $500,000 question incorrectly and lost $218,000, leaving him with only $32,000.
Duchovny provided the voice of Ethan Cole in the 2005 video game, Area 51, as well as that of the title character "XIII" in the 2003 video game XIII. In 2003, Duchovny starred in the 84th episode of the popular HBO show Sex And The City. He played the role of Jeremy, Carrie Bradshaw's high-school ex-boyfriend, who has committed himself to a Connecticut mental health facility. In 2005, Duchovny, who had already made his directorial debut with an episode of The X-Files, wrote, directed and featured in House of D. The film starred Anton Yelchin, Robin Williams and Duchovny's wife Tea Leoni in a coming-of-age tale. It received mostly poor reviews and little box office success. Duchovny also guest-directed an episode of Bones (Episode 211, "Judas on a Pole") during its second season.
Duchovny currently plays Hank Moody, a troubled novelist in Showtime's series Californication. The portrayal landed him a Golden Globe Award for Best Actor in a Television Comedy or Musical in 2007.
Duchovny is a former vegetarian.
On August 28, 2008 Duchovny's lawyer revealed that his client had checked himself into a rehabilitation facility for treating sex addiction.
| Year | Title | Role | Notes |
|---|---|---|---|
| 1988 | Working Girl | Tess' birthday party friend | |
| 1989 | New Year's Day | Billy | |
| 1990 | Denial | John | |
| Bad Influence | Club goer with glasses | ||
| 1991 | Twin Peaks | DEA Agent Denise/Dennis Bryson | TV series |
| Julia Has Two Lovers | Daniel | ||
| Don't Tell Mom the Babysitter's Dead | Bruce | ||
| The Rapture | Randy | ||
| 1992 | Ruby | Officer Tippit | |
| Beethoven | Brad | ||
| Baby Snatcher | David Anderson | TV movie | |
| Red Shoe Diaries | Jake Winters | TV series and movie | |
| Venice/Venice | Dylan | ||
| Chaplin | Rollie Totheroh | ||
| 1993 | Kalifornia | Brian Kessler | |
| The X-Files | FBI Special Agent Fox Mulder | TV series (1993-2002) | |
| 1995 | Saturday Night Live | Host | Episode 386, May 13, 1995 |
| 1996 | Space: Above and Beyond | Alvin EL 1543, a.k.a. "Handsome Alvin" | |
| 1997 | The Simpsons | FBI Special Agent Fox Mulder | TV series (One episode: "The Springfield Files") |
| Playing God | Dr. Eugene Sands | ||
| 1998 | The X-Files: Fight the Future | FBI Special Agent Fox Mulder | |
| Saturday Night Live | Host | Episode 446, May 9, 1998 | |
| 2000 | Return to Me | Bob Rueland | |
| 2001 | Evolution | Dr. Ira Kane | |
| Zoolander | J.P. Prewitt | ||
| 2002 | Full Frontal | Bill/Gus | |
| 2003 | Sex and the City | Jeremy | TV series (One episode: "Boy, Interrupted") |
| 2004 | Connie and Carla | Jeff | |
| House of D | Tom Warshaw | Directorial debut, also wrote film | |
| 2005 | Trust the Man | Tom | |
| 2006 | Pedigree Petfoods | Voice-over | "We're for dogs" ad campaign |
| The TV Set | Mike Klein | ||
| 2007 | Things We Lost in the Fire | Brian Burke | |
| The Secret (AKA Si j'étais toi'') | Dr. Benjamin Marris | ||
| Californication | Hank Moody | TV series | |
| 2008 | The X-Files: I Want to Believe | Fox Mulder | Filming finished on March 11, 2008, for a July 25, 2008 release |