A popular pilot episode, "My First Day." Intentionally mysterious, his real name is not known until the end of season 8, when he reveals it to be "Glenn Matthews." (This wouldn't necessarily be trustworthy information, were it not for the fact that creator and showrunner Bill Lawrence tweeted his official confirmation.)
The Janitor was played by Neil Flynn, who initially auditioned for the role of Dr. Cox but was instead given a smaller role that gradually expanded on the merits of his performance. Even on a show that encouraged improvisation, Flynn was especially known for ad-libbing many of his lines. One of the episode scripts was once even purported by Ted actor Sam Lloyd to have substituted the Janitor's dialogue with "Whatever Neil says." In addition to producing some truly memorable gags (for example, his fake doctor persona Dr. Ján Ĩtor), Flynn's performance helped accentuate the already bizarre nature of the Janitor character.
The theory and variations thereof have been posted by numerous Redditors and Scrubs fans, most of which state that the Janitor was a trained psychologist purposefully analyzing the doctors of Sacred Heart for secret research purposes. Some versions imagine him as being employed by the hospital for the benefit of his co-workers, whereas others position him as a disgraced former professional who toys with the doctors for his own amusement, all until J.D.'s departure leads to his resignation at the beginning of Scrubs season 9. These theories tend to cite the unusual level of control the Janitor has over his surroundings, his keen ability to manipulate people, and the multiple instances in which he is shown actually psychoanalyzing a person.
Granted, some points made in some of the posts don't entirely hold up as evidence. For instance, one claims that he is never seen doing any janitorial work, which isn't accurate. And, as pointed out by The Fugitive, suggesting that the Janitor may, in fact, be a retired actor (which, ittedly, does not rule out medical practice). However, there are many other points made that are completely able, like the idea that his antics are the result of boredom with his job caused by extreme overqualification.
Throughout the first season, the show's writers had planned to reveal that the Janitor was fake, a figment of J.D.'s imagination. While this idea was eventually scrapped, the ambiguity that it had required was only slowly chipped away from the character as the series progressed. So, ultimately, the idea that there was more to the Janitor than his chaotic surface let on is hard to prove or disprove, but, regardless of plausibility, it is a fun lens through which to view the character. It seems only appropriate that Scrubs, a show so versed in flipping the script between whimsical fantasy and grounded reality, would engender in its audience such imaginative discussions around the most fey, tricky, and inscrutable custodian in television history.