A genetic fingerprinting analysis of Caribbean isolates of M. avium complex (MAC) from AIDS patients by a Southern blotting technique after Pst1 digestion with nonradioactive DNA probes coding for single-copy sequences DT1 and DT6 was performed. In parallel, a selective amplification of a 187-bp fragment within the DT6 sequence with AV6/AV7 primers for Mycobacterium avium and of a 665-bp fragment within the DT1 sequence of M. intracellulare with the IN38/IN41 primers was also performed, and the molecular speciation with these two methods was compared with results obtained with DNA probes of the Accuprobe system. 66 strains investigated comprised 31 international reference isolates of MAC belonging to serovars 1-28 and 42-44, and 35 clinical isolates including 24 strains from Caribbean AIDS patients. 91.43% of the clinical isolates tested gave concordant data with the DT1/DT6 Southern hybridization and PCR as compared with 74.28% for PCR and Accuprobe, and 71.43% for Accuprobe and Southern hybridization. Our results corroborated previous findings showing that the DT1 probe was specific for M. intracellulare, whereas the DT6 probe was specific for M. avium (reference serovars 2 and 3 probed positive both with DT1 and DT6 probes). Contrary to DT1 probe, which did not reveal sufficient polymorphism to discriminate between MAC isolates, DT6 probe showed an interesting polymorphism giving four distinct clusters. Three clusters corresponded to profiles previously reported for reference and/or clinical isolates; however, a fourth cluster was discovered in five Caribbean isolates from four AIDS patients that did not correspond to previously published genetic patterns. When probed with the insertion sequence IS1245, this cluster retained its homogeneity.