In the early 1990s, severe enteritis caused by methicillin-resistant Staphylococcus aureus (MRSA enteritis) was prevalent in Japan, but the incidence has since decreased. We compared the genotypes and phenotypes of 12 isolates that caused MRSA enteritis (enteritis isolates), detected between 1990 and 1993, with 186 non-enteritis isolates detected between 1998 and 2002. Organisms were investigated using pulsed-field gel electrophoresis (PFGE), coagulase typing and reverse passive latex agglutination to detect production of staphylococcal enterotoxins (SE) and toxic shock syndrome toxin-1 (TSST-1); and polymerase chain reaction (PCR) for detection of the structural genes entA, entB, entC, entD and tst, which encode proteins SE-A, SE-B, SE-C, SE-D and TSST-1, respectively. The 12 enteritis isolates were classified into four types and four subtypes. Only seven of the 186 non-enteritis isolates had PFGE patterns indistinguishable from the enteritis isolates. Eight of the 12 enteritis isolates had entA, entC and tst, and produced high levels of SE-A and TSST-1, but not SE-C. Of the 186 non-enteritis isolates, 157 produced SE-C and TSST-1, but not SE-A. The seven non-enteritis isolates with a PFGE pattern indistinguishable from the enteritis isolates did not produce SE-A, and showed relatively low levels of TSST-1 production. These isolates may have continued to inhabit our ward since the earlier outbreak, but acquired a different phenotype. In conclusion, the disappearance of MRSA enteritis may have resulted from the decreased incidence of enteritis-causing clones and phenotypical changes.