Staphylococcus aureus produces exotoxins of the epidermal cell differentiation inhibitor (EDIN) family that ADP-ribosylate and inactivate Rho GTPases. The prevalence of genes encoding EDIN in clinical and nasal isolates of S. aureus was investigated. Of the 196 clinical S. aureus isolates tested, 15 (7.8%) were positive for 1 edin gene, whereas of 81 nasal isolates tested, only 3 (3.7%) were edin positive. Of the total 18 edin-positive isolates, 16 (90%) carried edin-B and 2 (10%) carried edin-C, but none was positive for edin-A. All edin-positive strains could produce the respective EDIN protein. Pulsed-field gel electrophoresis analysis suggested that the edin-B-positive S. aureus isolates are derived from one clone, and the edin-C-positive isolates are derived from another clone. Given that toxins acting on Rho GTPases are considered to be important for bacterial virulence, the EDIN toxins of S. aureus should receive more attention in future studies.