Mycobacterium avium complex (MAC) was originally composed of 2 species, M. avium and M. intracellulare. However, several new species closely related to M. intracellulare have recently been identified. In addition, M. avium has been further subdivided into 4 subspecies. The aim of this study was to determine the proportion of different MAC species recovered from respiratory specimens and to elucidate the clinical relevance of these species. Clinical isolates, from 219 patients, that had been initially identified as M. avium or M. intracellulare by non-sequencing methods were reidentified using multilocus sequence typing, and the clinical significance of the identified species was then investigated. Of 91 isolates originally identified as M. intracellulare, 75 (82%) were confirmed to be M. intracellulare, 8 (9%) isolates were identified as M. chimaera, and 4 (4%) isolates each were identified as "M. indicus pranii" and M. yongonense. The 128 isolates originally designated as M. avium were determined to be M. avium subsp. hominissuis. Of the 219 patients, 146 (67%) met the diagnostic criteria for MAC lung disease, and for each MAC species, the proportion of patients meeting these criteria was as follows: M. intracellulare (54/75, 72%), M. chimaera (3/8, 38%), "M. indicus pranii" (3/4, 75%), M. yongonense (2/4, 50%), and M. avium subsp. hominissuis (84/128, 66%). In summary, multilocus sequence typing of respiratory isolates initially identified as MAC revealed that, although most isolates were M. avium subsp. hominissuis or M. intracellulare, approximately 7% were newer MAC members, with clinical evidence supporting their potential pathogenicity for humans.