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| Award | Year (↓) | Category | Nominee / Winner | Person |
|---|---|---|---|---|
| Screen Actors Guild Award | 2000 | Outstanding Performance by an Actor in a Television Drama Series | Nominee | David Duchovny |
| Screen Actors Guild Award | 2000 | Outstanding Performance by an Actress in a Television Drama Series | Nominee | Gillian Anderson |
| TV Guide Award (televised) | 2000 | Favorite Actor in a Drama Series | Nominee | David Duchovny |
| Teen.com Entertainment Award | 2000 | Best TV Drama Series | Winner | |
| Teen.com Entertainment Award | 2000 | Best TV Actress | Winner | Gillian Anderson |
| Cadet Award | 2000 | Outstanding Writing in a Drama Series | Nominee | Vince Gilligan |
| TV Guide Award (televised) | 2000 | Favorite Actress in a Drama Series | Nominee | Gillian Anderson |
| Saturn Award | 2000 | Best Network Television Series | Nominee | |
| Saturn Award | 2000 | Best Television Actress | Nominee | Gillian Anderson |
| Cadet Award | 2000 | Outstanding Cinematrography | Nominee | |
| Petcabus Award | 2000 | Best Guest Actor or Actress in a Comedy or Drama Series | Nominee | Tea Leoni |
| Online Television Academy Award | 2000 | Best Makeup and Hair in a Television Series | Nominee | |
| RATTY Award | 2000 | Series that Most Went Downhill | Nominee | |
| Cadet Award | 2000 | Outstanding Sound | Nominee | |
| Online Television Academy Award | 2000 | Best Sound in a Television Series | Nominee | |
| Online Television Academy Award | 2000 | Best Visual Effects in a Television Series | Nominee | |
| Golden Reel Award (MPSE) | 2000 | Outstanding Editing of Dialogue and Automated Dialogue Replacement (A.D.R.) in Episodic Television | Nominee | |
| Cadet Award | 2000 | Outstanding Music Composition | Nominee | |
| TV Guide Award (televised) | 2000 | Favorite Sci-Fi/Fantasy Show | Nominee | |
| Electronic Media's Critics Poll | 1999.07 | Best Television Series (#17) | Winner | |
| Electronic Media's Critics Poll | 1999.01 | Best Television Series (#17) | Winner | |
| Petcabus Award | 1999 | Best Actress in a Drama Series | Nominee | Gillian Anderson |
| Golden Laurel Award | 1999 | Nova Award for Television | Winner | Chris Carter |
| Online Television Academy Award | 1999 | Best Sound in a Television Series | Winner | |
| Online Television Academy Award | 1999 | Best Visual Effects in a Television Series | Nominee | |
| Online Television Academy Award | 1999 | Best Episode in a Drama Series | Nominee | |
| RATTY Award | 1999 | Best Science Fiction/Fantasy Series | Nominee | |
| Cadet Award | 1999 | Outstanding Directing in a Drama Series | Nominee | Chris Carter |
| SyFy Genre Award | 1999 | Best Series | Winner | |
| ASCAP Film & TV Music Award | 1999 | Top Television Series | Winner | Mark Snow |
| Golden Reel Award (MPSE) | 1999 | Outstanding Editing of Dialogue and Automated Dialogue Replacement (A.D.R.) in Episodic Television | Nominee | |
| EW's All Time Greatest/Worst Lists | 1999 | 100 Greatest TV Moments (#37) | Winner | |
| Emmy Award | 1999 | Outstanding Art Direction for a Series | Nominee | |
| Golden Reel Award (MPSE) | 1999 | Outstanding Music Editing in Episodic Television | Nominee | |
| Emmy Award | 1999 | Outstanding Cinematography for a Series | Nominee | Bill Roe |
| Cadet Award | 1999 | Outstanding Cinematography | Nominee | |
| Cadet Award | 1999 | Outstanding Sound | Nominee | |
| RATTY Award | 1999 | Best Lead Actor in a Science Fiction Series | Winner | David Duchovny |
| American Cinematographers Award | 1999 | Outstanding Cinematography in a Television Series | Winner | Bill Roe |
| RATTY Award | 1999 | Best Lead Actress in a Science Fiction Series | Winner | Gillian Anderson |
| Online Television Academy Award | 1999 | Best Drama Series | Nominee | |
| Cadet Award | 1999 | Outstanding Costume Design | Nominee | |
| Golden Globe Award | 1999 | Outstanding Television Drama Series | Nominee | |
| TV Times Readers' Choice | 1999 | Best Actor in a Drama (#1) | Voted | David Duchovny |
| RATTY Award | 1999 | Best Writing in a Science Fiction Series | Winner | David Duchovny |
| Golden Globe Award | 1999 | Outstanding Actor in a Television Drama Series | Nominee | David Duchovny |
| Emmy Award | 1999 | Outstanding Guest Actress in a Drama Series | Nominee | Veronica Cartwright |
| Online Television Academy Award | 1999 | Best Lead Actress in a Drama Series | Nominee | Gillian Anderson |
| Entertainment Weekly's Best/Worst List | 1999 | The Ten Best (#7) | Winner | |
| Golden Globe Award | 1999 | Outstanding Actress in a Television Drama Series | Nominee | Gillian Anderson |
