Jennifer Garner's opening narration, which was used throughout season one, was literally phoned in. She was working on-___location, and had to read it on the phone to J.J. Abrams, who was recording it on the other end.
Will Tippin's sister, seen briefly in the pilot episode, "Truth Be Told" and several other episodes, was played by Jennifer Garner's stand-in, Nancy Wetzel.
The two children who say "Bad robot!" in the Bad Robot logo are the children of series creator and executive producer J.J. Abrams.
Greg Grunberg's character was named Eric Weiss. Erich Weiss was the birth name of Harry Houdini. Will Tippin (Bradley Cooper) mentioned this fact when he and Weiss met in season two, episode twenty-two, "The Telling".
SD in SD-6 stands for Section Disparue, the section that has "disappeared".