Clinical isolates of Mycobacterium avium (n=81) from patients with pulmonary infections who were HIV-negative and isolates (n=33) from HIV-positive patients were subjected to genetic analysis by PCR detection of three M. avium-specific insertion sequences (IS901, IS1245 and IS1311), and nucleotide sequencing of the heat-shock protein 65 (hsp65) gene. All clinical isolates were identified as 'M. avium subspecies hominissuis' by sequence analysis of hsp65. Compared with clinical isolates of M. avium reported elsewhere, IS1245 was found less frequently in Japanese isolates (96/114 isolates, 84%) and IS901 was detected more frequently (76/114 isolates, 67%). One isolate was found to lack IS1311, which has not been reported previously for 'M. avium subsp. hominissuis'. Nucleotide sequence analysis of the PCR products for IS901 revealed that all clinical isolates had the same new insertion sequence, designated ISMav6, which had 60 point mutations compared with the nucleotide sequence of the original IS901. These results suggest that 'M. avium subsp. hominissuis' with ISMav6 is prevalent in Japan. ISMav6 may have implications for the virulence of M. avium and contribute to an increase of M. avium infections in this country.