OBJECTIVE Isolates of M. tuberculosis were analyzed for their DNA fingerprints to facilitate understanding of ongoing transmission of tuberculosis in Sapporo (population 1.87 million), Japan, where the incidence rate of tuberculosis was 15.0 per 100,000 in 2004. METHODS Out of all tuberculosis patients registered in the city from November 1998 to December 2003, isolates from culture-positive respiratory tuberculosis cases for whom written informed consent had been obtained, were analyzed by restriction fragment length polymorphism (RFLP). The study included 345 cases (249 men and 96 women) whose isolates were available for DNA patterns. METHODS Using standard IS6110-RFLP typing, cases whose isolates shared identical fingerprints were considered to belong to the same cluster. Proportions of clustered cases were evaluated according to their clinical and socio-economical characteristics. RESULTS Out of 345 cases, 207 (60.0%) were classified into 59 clusters, and 15% of clustered cases having definite epidemiological links. Multiple logistic regression analysis in men showed that age and infectiousness were significantly related to clustering. The adjusted odds ratios (OR) [95% confidence intervals (CI)] were 0.17 [0.03-0.79] for 30-59 years, 0.15 [0.03-0.69] for 60 years or over and 2.35 [1.17-4.70] for those cases assigned as the highest level of transmission of tuberculosis from the infectiousness index of cases. For women the final model showed the adjusted OR [95% CI] were 0.52 [0.22-1.22] for those with previous history of tuberculosis and 0.33 [0.06-1.85] for diabetics. In male cases with a previous history of tuberculosis, most highly infectious cases were significantly associated with clustering (OR [95% CI], 4.53 [1.16-17.68]). CONCLUSIONS The results suggest that highly infectious male tuberculosis cases with endogenous reactivation have contributed to recent transmission of tuberculosis in the studied area.