To further understand the molecular and clinical epidemiology of tuberculosis in the Toronto Somali community, molecular fingerprinting using IS6110 restriction fragment length polymorphism typing or spoligotyping was performed on M. tuberculosis isolates obtained from Somali-Canadians who developed active disease from 1997 to 2001. Molecular fingerprints were further compared with those obtained from Somalis residing in Denmark. 142 Somali TB patients were reported, for whom, 80 isolates were fingerprinted. 25% of isolates were clustered. Three clusters involving 2 patients each were identified out of the17 isolates that underwent spoligotyping. Of the 63 isolates typed by the IS6110 method, 6 clusters (4 of 2 patients and 2 of 3 patients) were identified. 57% of these isolates were found to be identical to Danish isolates. Our study suggests that a combination of reactivation and recent transmission are responsible for the high incidence rates of tuberculosis in this community. We recommend that ongoing surveillance and treatment programmes be directed towards this community.