A total of 75 Staphylococcus aureus isolates associated with food-borne diseases, food samples, healthy human feces and human nasal swabs were examined for the presence of 20 kinds of classical and newly identified staphylococcal enterotoxin (SE), and enterotoxin-like (SEl) genes (SE/SEl genes: sea-selu) by PCR. Multiple SE/SEl gene types were detected from 70.7% of isolates. All isolates associated with food-borne disease produced classical SE, but some of them harbored several newly identified SE and SEl genes in addition to classical SE gene. Isolates associated with food samples, healthy human feces and human nasal swabs showed multiple SE/SEl gene types, and some of them harbored only newly identified SE and/or SEl gene. Detection of SE/SEl genes by PCR was also shown to be useful for epidemiological study of S. aureus.