A total of 33 clinical isolates of the Mycobacterium avium complex from 25 patients, identified by means of biochemical and cultural characteristics, the Accuprobe system and DT1/DT6 PCR, were further analysed using novel insertion elements IS1245 and IS1311 in a French Caribbean setting. PvuII-cleaved DNA and non-radioactive Southern hybridization and detection systems were used for fingerprinting with both IS elements. The data confirmed the specificity of the two probes for M. avium in our setting and highlighted a significant proportion of M. intracellulare-infected patients in this region. Two distinct groups composed of 2-3 bands and 6-27 bands were found among M. avium isolates, and were composed of the same isolates both with IS1245 and IS1311. The computer analysis of polymorphic banding patterns identified two prevalent genotypes: one contained 4 isolates from 3 patients while a second 2-banded cluster was composed of 6 isolates from 4 patients; all the patients were from the same hospital in Guadeloupe. A single isolate from Martinique was falsely included in the 2-banded cluster initially upon IS1245 fingerprinting, but could be discriminated from other isolates on the basis of IS1311 fingerprinting of PvuII-cleaved DNA. These results were also confirmed upon IS1245 fingerprinting of PstI-digested DNA, as well as DT6 fingerprinting. A single case of polyclonal infection was also discovered in a patient at a 75-day interval. This is the first study comparing the two IS elements and constitutes a first description of disseminated M. avium complex disease from the Caribbean. We conclude that both elements possess a similar discriminatory potential for M. avium isolates. Coupled with computer analysis, this methodology would appear to be particularly suitable for larger epidemiological studies.