Initially, the janitor was to be a figment of J.D.’s imagination of the show were to be cancelled within the first two seasons. It would have been revealed in the finale. The janitor seems to be acknowledged by other hospital employees in the first season. 
They would have been explained as pure coincidence or as part of interactions in J.D.’s imagination. The first time the janitor has any real interaction with other employees is in season 2 when he blackmails Turk and J.D. in “My Karma.” Since the start of season 2, the janitor became a main cast member and had regular interactions with other main characters. The janitor even had an entire episode devoted to him.