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| Award | Year (↓) | Category | Nominee / Winner | Person |
|---|---|---|---|---|
| Directors Guild Award | 1999 | Outstanding Directorial Achievement in Television Drama Series | Nominee | Chris Carter |
| TV Times Readers' Choice | 1999 | Best Actress in a Drama (#1) | Voted | Gillian Anderson |
| RATTY Award | 1999 | Best Directing in a Science Fiction Series | Winner | Chris Carter |
| Environmental Media Association Award | 1999 | Television Episodic Drama | Winner | Daniel Arkin |
| Art Directors Guild Award | 1999 | Excellence in Production Design in Television | Winner | Corey Kaplan |
| Emmy Award | 1999 | Outstanding Lead Actress in a Drama Series | Nominee | Gillian Anderson |
| TV Guide Award (televised) | 1999 | Favorite Actor in a Drama Series | Winner | David Duchovny |
| International Horror Guild Award | 1999 | Best Horror Television Series | Nominee | |
| Golden Satellite Award | 1999 | Best Television Drama Series | Nominee | |
| Golden Satellite Award | 1999 | Best Actress in a Television Drama Series | Nominee | Gillian Anderson |
| Emmy Award | 1999 | Outstanding Makeup for a Series | Winner | |
| TV Guide Award (televised) | 1999 | Favorite Actress in a Drama Series | Nominee | Gillian Anderson |
| Emmy Award | 1999 | Outstanding Music Composition for a Series | Nominee | Mark Snow |
| Emmy Award | 1999 | Outstanding Single-Camera Editing for a Series | Nominee | |
| Screen Actors Guild Award | 1999 | Outstanding Performance by an Actor in a Television Drama Series | Nominee | David Duchovny |
| Emmy Award | 1999 | Outstanding Sound Editing for a Series | Nominee | |
| Screen Actors Guild Award | 1999 | Outstanding Performance by an Actress in a Television Drama Series | Nominee | Gillian Anderson |
| TV Guide Award (televised) | 1999 | Favorite Drama Series | Nominee | |
| Screen Actors Guild Award | 1999 | Outstanding Performance by an Ensemble in a Television Drama Series | Nominee | |
| Online Television Academy Award | 1999 | Best Direction in a Drama Series | Nominee | |
| Saturn Award | 1999 | Best Network Series | Winner | |
| Saturn Award | 1999 | Best Television Actor | Nominee | David Duchovny |
| Viewers for Quality Television Award | 1999 | Best Actress in a Quality Drama Series | Winner | Gillian Anderson |
| Online Television Academy Award | 1999 | Best Writing in a Drama Series | Nominee | |
| Saturn Award | 1999 | Best Television Actress | Nominee | Gillian Anderson |
| BAFTA TV Award | 1999 | Best International Programme or Series | Nominee | |
| Online Television Academy Award | 1999 | Best Scoring in a Television Series | Nominee | |
| Cadet Award | 1999 | Outstanding Lead Actor in a Drama Series | Nominee | David Duchovny |
| Cadet Award | 1999 | Outstanding Lead Actress in a Drama Series | Nominee | Gillian Anderson |
| Petcabus Award | 1999 | Best Drama Series | Nominee | |
| Online Television Academy Award | 1999 | Best Editing in a Television Series | Nominee | |
| Online Television Academy Award | 1999 | Best Cinematography in a Series | Winner | |
| Online Television Academy Award | 1999 | Best Production Design in a Television Series | Nominee | |
| Electronic Media's Critics Poll | 1998.07 | Best Television Series (#10) | Winner | |
| Electronic Media's Critics Poll | 1998.01 | Best Television Series (#3) | Winner | |
| Emmy Award | 1998 | Outstanding Drama Series | Nominee | |
| Online Television Academy Award | 1998 | Best Scoring in a Television Series | Winner | |
| Emmy Award | 1998 | Outstanding Guest Actress in a Drama Series | Nominee | Lili Taylor |
| Emmy Award | 1998 | Outstanding Guest Actress in a Drama Series | Nominee | Veronica Cartwright |
| Online Television Academy Award | 1998 | Best Editing in a Television Series | Winner | |
| Cadet Award | 1998 | Outstanding Drama Series | Nominee | |
| Online Television Academy Award | 1998 | Best Cinematography in a Series | Winner | |
| Emmy Award | 1998 | Outstanding Lead Actor in a Drama Series | Nominee | David Duchovny |
| ASCAP Film & TV Music Award | 1998 | Top Television Series | Winner | Mark Snow |
| Emmy Award | 1998 | Outstanding Lead Actress in a Drama Series | Nominee | Gillian Anderson |
| Golden Reel Award (MPSE) | 1998 | Outstanding Sound Editing in Episodic Television | Winner | |
| Online Television Academy Award | 1998 | Best Sound in a Television Series | Winner | |
| Online Television Academy Award | 1998 | Best Television Series | Winner | |
| Online Television Academy Award | 1998 | Best Visual Effects in a Television Series | Nominee | |
| Cinema Audio Society Award | 1998 | Outstanding Achievement in Sound Mixing for a Television Series | Nominee | David John West, Kurt Kassulke |
