The application of molecular techniques to investigate strain relatedness may help define the local epidemiology of Mycobacterium avium infection, and, by identifying false isolates (i.e. neither pathogens nor colonizers) resulting from contamination, may serve as a tool for quality control in the laboratory. For this purpose, isolates from all patients (n = 129) with Mycobacterium avium infections identified over a two-year period were investigated by pulsed-field gel electrophoresis (PFGE). Of 38 PFGE patterns identified, 34 corresponded to unique strains or to isolates present in no more than two or three individuals. One prevalent strain was identified among HIV-infected patients and three patterns were related to culture contamination events. PFGE (i) established the diversity of Mycobacterium avium strains in a community; (ii) identified the existence of a unique strain that may account for one-fifth of Mycobacterium avium isolated from HIV-infected patients locally; (iii) documented the extent and resolution of a suspected pseudo-outbreak; and (iv) uncovered an additional-unsuspected contamination event.