No one knows yet! Some have claimed that they've heard the name "Tom" or "Ryan", such as in the "My Buddy's Booty" episode, where a co-worker of the Janitor applauds him for a "zinger" towards Dr. Cox, but these have not been confirmed. Some say that because of the episode where the Janitor was seen in "The Fugitive" that his name is, of course, Neil Flynn. Neil himself has stated in an interview that the Janitor's name is NOT Neil Flynn, nor is the Janitor's name Jan Itor. Bill Lawrence said in a recent interview that in the 7th and final season Janitor will get what Neil Flynn has asked for for years: a girlfriend and a name. In the 7th Season, the Janitor hinted that his real name was Josh, when referring to the many things (sometimes insults) that people have called him by. In an interview, Neil jokingly said the Janitor's name was "Zanzibar Buck-Buck McFake". Bill Lawrence has also stated the Janitor's name is that of the Janitor character on his short-lived animated series, "Clone High". On this show the Janitor is clearly referred to as "Glen" in at least one episode. Coincidentally , Neil Flynn was the voice of Glen the Janitor, among other characters, on "Clone High."
On the finale, JD asks Janitor his name, and he claims it is Glen Matthews. However, when JD walks away, another person walks by and says "Hey Tommy", to which the janitor responds. So, it is now up to the viewer to decide if they believe he was telling JD the truth or not, but going by the "Clone High" clue, it is entirely possible that that is his name.
According to Bill Lawrence on the bonus disc of the complete series the Janitor's name IS Glen Matthews