A heterogenic group of staphylococcal exotoxins, including staphylococcal superantigenic toxins, enterotoxin (SE), toxic shock syndrome toxin-1 (TSST-1), and coagulase are the most important virulence factors of Staphylococcus aureus. We analyzed the prevalence of genes encoding five enterotoxins and TSST-1 in S. aureus isolated from clinical ear discharges. The genes were identified by multiplex PCR and we compared the results to references of coagulase serotypes. In 102 isolates of S. aureus, 44 of them were methicillin-resistant S. aureus (MRSA) and the others were methicillin-susceptible S. aureus (MSSA). Among both types of S. aureus, 33 strains were positive for sea, 2 for seb, 23 for sec, 26 for see, and 26 for tst. Overall, 59 (57.8%) isolates were positive for one or more superantigenic toxin genes. From these, 71.2% (42/59) strains harbored more than one toxin gene in different combinations. The major combinations of genes were sea and see, and sec and tst. The degree of possession of superantigenic toxic genes was similar in both MRSA and MSSA isolates (56.8% vs 58.6%, respectively), yet significant differences in toxin gene profiles and coagulase serotypes between two isolates were detected. All of 13 positive strains for sec and tst were MRSA and belonged to coagulase serotype II. On the other hand, 80.0% of 20 positive strains for sea and see were MSSA with coagulase serotype IV and VII, whereas 20.0% of them were MRSA with coagulase serotype IV. This data indicates that the profile of superantigenic toxin genes correlates to coagulase serotype and methicillin resistance in S. aureus isolates.