Chris Carter finished putting the pilot together at 5am, ready for screening to the Fox executives at 8 that very same morning. Fortunately his pilot was greeted with spontaneous applause from his audience.
It is rumored that the infamous homecoming photo of Laura Palmer from Twin Peaks (1990) can be seen on Mulder's office wall in this episode. _David Duchovny_ had a prominent multi-episode guest starring arc in the second season of the earlier series.
The trivia items below may give away important plot points.
The closing scenes of Pilot are almost identical to the closing scenes of the season finale, The X-Files: The Erlenmeyer Flask (1994). Scully is in bed and sees her digital clock turn from 11:21 to 11:22. Mulder calls and they talk. The scene cuts to The Cigarette Man, who places an object in the vast Pentagon vault. Both episodes end with the door of the vault slamming shut and the camera showing the sign on the door: "In Case Of Fire Or Emergency / Know Your Exits / PENTAGON / Evacuation Procedure."
According to Chris Carter, the first time that Mulder fell for Scully was when she came in his office for the first time and the first time she did it was when they talked by the phone at the end of the episode. It's something remarkable coming from him, since he is not known by his shipper feeling with Mulder and Scully.