Mycoplasma pneumoniae clinical isolates obtained between 1995 and 2005 were examined to determine the prevalent genotype. One hundred and twenty-seven strains isolated from bronchitis and pneumonia patients were genotyped by a PCR-RFLP method based on nucleotide sequence polymorphisms of the p1 gene, which encodes the major adhesin protein. The typing results established that 66 of the isolates were group I strains, 45 were group II strains and 16 were group II variants. Analysis of the annual occurrence of these isolates showed a predominance of group II strains between 1995 and 2001 (n=37). No group I strain was found during this period. However, group I strains appeared in the isolates from 2002 (2/5 isolates, 40 %) and increased in specimens taken after 2003, thereby constituting a large proportion of the isolates. In 2004 and 2005, no group II strains were found among the isolates (n=49), although there were nine group II variants. Throat swabs and sputum samples obtained from patients with respiratory infections between 1997 and 2005 were also analysed by PCR-RFLP or a new nested PCR to detect the p1 gene DNA. Typing analysis of these p1 gene DNAs also showed that the group I p1 gene was not present in specimens taken before 2000, but was present and dominant in specimens taken after 2001. These results indicate that, in Japan, the prevalent type of M. pneumoniae changed from a group II strain to a group I strain around 2002.