- Peanuts: When Stan spots Wendy in the cafeteria, he smiles similarly to Charlie Brown when he sees the Little Red Haired Girl.
- I Love to Singa: Cartman sings this song from the eponymous cartoon when an alien spaceship struck him with a laser.
- A few later copies of the South Park: The Complete Second Season boxsets are bundled with a fourth disc called South Park: The Original Unaired Pilot, centered around this episode entirely.
- Trey Parker's first name is misspelled in the intro twice, as "Tre" and "Tres".
- Trey Parker and Matt Stone respectively credit themselves as "Tupac Schwartz" and "M.C. Goldstein" in the opening credits.
- The episode was available for viewing on South Park Studios for a limited time, from mid-August to mid-September 2009. It is no longer available for viewing.
- The Pilot and its aired version are the only full length episodes with stop motion animation on construction paper.
- Wendy's voice is lower than in the aired pilot. This is probably because Mary Kay Bergman did not voice any of the female characters, including Wendy. They were all voiced by Karri Turner.
- Cartman has a sister and father in this episode. They were removed from the television series.
- Nurse Gollum does not have a conjoined fetus and is absent from "Cartman Gets an Anal Probe"; her official televised debut was the Season 2 episode "Conjoined Fetus Lady".
Kyle tosses a rock at a UFO, which in response fires a laser at Kenny. He is flung into the road. Kenny survives, but then a herd of cows run him over. Kenny also manages to survive from them, but then Officer Barbrady drives his police car over him by accident, killing him.