| 2 | — | 4x01: Herrenvolk | - | Base card | — | — |
| 3 | — | 4x02: Unruhe | - | Base card | — | — |
| 4 | — | 4x03: Home | - | Base card | — | — |
| 5 | — | 4x04: Teliko | - | Base card | — | — |
| 6 | — | 4x05: The Field Where I Died | - | Base card | — | — |
| 7 | — | 4x06: Sanguinarium | - | Base card | — | — |
| 8 | — | 4x07: Musings of a Cigarette-Smoking Man | - | Base card | — | — |
| 9 | — | 4x08: Paper Hearts | - | Base card | — | — |
| 10 | — | 4x09: Tunguska | - | Base card | — | — |
| 11 | — | 4x10: Terma | - | Base card | — | — |
| 12 | — | 4x11: El Mundo Gira | - | Base card | — | — |
| 13 | — | 4x12: Kaddish | - | Base card | — | — |
| 14 | — | 4x13: Never Again | - | Base card | — | — |
| 15 | — | 4x14: Leonard Betts | - | Base card | — | — |
| 16 | — | 4x15: Memento Mori | - | Base card | — | — |
| 17 | — | 4x16: Unrequitted | - | Base card | — | — |
| 18 | — | 4x17: Tempus Fugit | - | Base card | — | — |
| 19 | — | 4x18: Max | - | Base card | — | — |
| 20 | — | 4x19: Synchrony | - | Base card | — | — |
| 21 | — | 4x20: Small Potatoes | - | Base card | — | — |
| 22 | — | 4x21: Zero Sum | - | Base card | — | — |
| 23 | — | 4x22: Elegy | - | Base card | — | — |
| 24 | — | 4x23: Demons | - | Base card | — | — |
| 25 | — | 4x24: Gethsemane | - | Base card | — | — |
| 26 | — | 5x01: Unusual Suspects | - | Base card | — | — |
| 27 | — | 5x02: Redux | - | Base card | — | — |
| 28 | — | 5x03: Redux II | - | Base card | — | — |
| 29 | — | 5x04: Detour | - | Base card | — | — |
| 30 | — | 5x05: Christmas Carol | - | Base card | — | — |
| 31 | — | 5x06: Post-Modern Prometheus | - | Base card | — | — |
| 32 | — | 5x07: Emily | - | Base card | — | — |
| 33 | — | 5x08: Kitsunegari | - | Base card | — | — |
| 34 | — | 5x09: Schizogeny | - | Base card | — | — |
| 35 | — | 5x10: Chinga | - | Base card | — | — |
| 36 | — | 5x11: Kill Switch | - | Base card | — | — |
| 37 | — | 5x12: Bad Blood | - | Base card | — | — |
| 38 | — | 5x13: Patient X | - | Base card | — | — |
| 39 | — | 5x14: The Red and the Black | - | Base card | — | — |
| 40 | — | 5x15: Travelers | - | Base card | — | — |
| 41 | — | 5x16: Mind’s Eye | - | Base card | — | — |
| 42 | — | 5x17: All Souls | - | Base card | — | — |
| 43 | — | 5x18: The Pine Bluff Variant | - | Base card | — | — |
| 44 | — | 5x19: Folie A Deux | - | Base card | — | — |
| 45 | — | 5x20: The End | - | Base card | — | — |
| 46 | — | Special Agent Fox Mulder | - | Base card | — | — |
| 47 | — | Special Agent Dana Scully | - | Base card | — | — |
| 48 | — | Assistant Director Skinner | - | Base card | — | — |
| 49 | — | John Fitzgerald Byers | - | Base card | — | — |
| 50 | — | Melvin Frohike | - | Base card | — | — |
| 51 | — | Ringo Langly | - | Base card | — | — |
| 52 | — | Emily Sim | - | Base card | — | — |
| 53 | — | Samantha Mulder | - | Base card | — | — |
| 54 | — | Max Fenig | - | Base card | — | — |
| 55 | — | The Cigarette-Smoking Man | - | Base card | — | — |
| 56 | — | The Well-Manicured Man | - | Base card | — | — |
| 57 | — | The First Elder | - | Base card | — | — |
| 58 | — | Marita Covarrubias | - | Base card | — | — |
| 59 | — | Alex Krycek | - | Base card | — | — |
| 60 | — | Mrs. Mulder | - | Base card | — | — |
| 61 | — | Agency Danny Pendrell | - | Base card | — | — |
| 62 | — | Jeremiah Smith | - | Base card | — | — |
| 63 | — | Alien Bounty Hunter | - | Base card | — | — |
| 64 | — | Thoughtograph Terror | - | Base card | — | — |
| 65 | — | The Melanin-Suckre | - | Base card | — | — |
| 66 | — | The Face-Lifter | - | Base card | — | — |
| 67 | — | A Picture Is Worth… | - | Base card | — | — |
| 68 | — | All Bets Are Off | - | Base card | — | — |
| 69 | — | Now You See Him… | - | Base card | — | — |
| 70 | — | Frozen Stiff | - | Base card | — | — |
| 71 | — | When Babies Had Tails | - | Base card | — | — |
| 72 | — | Phantom Lady | - | Base card | — | — |
| 73 | — | Don’t Fool with Mother Nature | - | Base card | — | — |
| 74 | — | Man-Made Monster | - | Base card | — | — |
| 75 | — | Return of the Pusher | - | Base card | — | — |
| 76 | — | Mud Sucker | - | Base card | — | — |
| 77 | — | The Doll From Hell | - | Base card | — | — |
| 78 | — | Mulder the Vampire Slayer | - | Base card | — | — |
| 79 | — | The Secret Invasion | - | Base card | — | — |
| 80 | — | Guardian Angel | - | Base card | — | — |
| 81 | — | Skinner…Bugged | - | Base card | — | — |
| 82 | — | Pileggi Briefs | - | Base card | — | — |
| 83 | — | Monster Maker | - | Base card | — | — |
| 84 | — | To Bee or Not to Bee | - | Base card | — | — |
| 85 | — | Everywhere an E.T. | - | Base card | — | — |
| 86 | — | Filming an Autopsy | - | Base card | — | — |
| 87 | — | Fabricating a Forest Creature | - | Base card | — | — |
| 88 | — | Munch-ing on the Set | - | Base card | — | — |
| 89 | — | Shining Directors | - | Base card | — | — |
| 90 | — | Checklist | - | Base card | — | — |
| A1 | — | Chris Carter - Series Creator and Executive Producer | Autographs | Chase Card | — | — |
| A2 | — | Bruce Harwood as John Fitzgerald Byers | Autographs | Chase Card | — | — |
| A3 | — | Jerry Hardin as Deep Throat | Autographs | Chase Card | — | — |
| A4 | — | Laurie Holden as Marita Covarrubias | Autographs | Chase Card | — | — |
| A5 | — | Brendan Beiser as Agent Pendrell | Autographs | Chase Card | — | — |
| B1 | — | Eyeball | Black Oil | Chase Card | — | — |
| B2 | — | Scully In Hazards Suit | Black Oil | Chase Card | — | — |
| B3 | — | Mulder And Krycek | Black Oil | Chase Card | — | — |
| B4 | — | Mulder In Agony | Black Oil | Chase Card | — | — |
| B5 | — | Mulder Netted | Black Oil | Chase Card | — | — |
| B6 | — | Conspirators | Black Oil | Chase Card | — | — |
| D1 | — | Ace of Hearts | Death Cards | Chase Card | — | — |
| D2 | — | King of Hearts | Death Cards | Chase Card | — | — |
| D3 | — | Queen of Hearts | Death Cards | Chase Card | — | — |
| P1 | — | Mulder in Net | I Want to Believe | Chase Card | — | — |
| P2 | — | Mulder in Robe | I Want to Believe | Chase Card | — | — |
| P3 | — | Mulder with Umbrella | I Want to Believe | Chase Card | — | — |
| PC1 | — | Mulder and Scully | Dealers | Promo Card | — | — |
| PC2 | — | Lone Gunmen | Non-Sport Update Magazine | Promo Card | — | — |
| Pi | — | Government Conspiracy | Website Promo | Promo Card | — | — |
| PW1 | — | Sweatshirt worn by David Duchovny as Fox Mulder | Pieceworks | Chase Card | — | — |
| XBL-1 | — | Scully and Mulder | Box Loader | Chase Card | — | — |
| XCL-1 | — | Scully | Case Loader | Chase Card | — | — |
| XM-1 | — | Scully and Mulder | X-Files Magazine | Promo Card | — | — |
