This production has not been approved, endorsed or authorized by the Federal Bureau of Investigation. (appears in the end credits)
The opening credits of the first 7 seasons include an extreme close-up of an eye blinking. In the 8th season credits, the eye belongs to Gillian Anderson.
In the main title for the ninth season, a piece of paper flashes across the screen listing "FBI Contacts: Witnesses and Contributors." The names on the list are screen names of the series' on-line fans. For episodes #9.01-#9.11, the names were randomly picked from various X-Files message boards. For episodes #9.12-#9.19, the names came from contest entries.
Occasionally, the phrase "The Truth Is Out There" in the opening credits has been changed to something else, for example "Trust No One" or "Apology is Policy".
In the main title sequence, the man in the photo pointing to the UFO in the shadowy night sky is Bruce Bryant -- one of the main title designers. He's also the stand-in for the wispy translucent ghost, shot using a negative effect in the hallway of their offices.
Beginning from season 03, the opening title sequence reduced its run time for the episodes dealing with Mulder and Scully's personal life.
At the end of the credits, the logo for Ten Thirteen Productions is shown, and a child's voice says "I made this!"