This episode was originally intended to be aired as the third episode of the season on October 16. NBC changed their scheduling as to not compete new episodes of Friends and Scrubs against the 2003 Yankees/Marlins World Series on Fox. Rather than airing this episode the following week, NBC moved on to episode #304 ("My White Whale") and bumped "My Dirty Secret" to December 11. Minor changes to J.D.'s inner monologue were made to fit update the episode in this season's story line. Near the beginning, for example, J.D.'s comment that "Elliot's boyfriend is back for the weekend while mine is away," was originally just, "Ah, Elliot and her marine biologist boyfriend are at it again. But you know what? It honestly doesn't bother me."