My Day Off - S1-E9
Corrected entry: When J.D. has his appendectomy, Turk is cutting on his left side. The appendix is on the right side of the body. Ironically, J.D. is commenting in the voice-over about what a great surgeon Turk is.
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Correction: About one in 10,000 people have 'situs inversus', a total reversal of their organs. In such a case, the appendix would be on the left. See here: http://en.wikipedia.org/wiki/Situs_inversus.
During the surgery Turk was cutting on the left side later in the episode he came to check on JD and the bandages and the scar were on the right side.