The propensity of Mycobacterium tuberculosis genotypes to spread across geographic boundaries was investigated by comparing the IS6110 and polymorphic GC-rich sequence patterns of M. tuberculosis isolates from San Francisco and the East Bay, two distinct regions separated by San Francisco Bay. Of 724 isolates from incident tuberculosis patients during 1992 and 1993, only 53 (7.3%) had patterns matching ≥1 isolates from the other region. In the multivariable analysis of patient risk factors, an AIDS diagnosis (odds ratio [OR], 1.89; 95% confidence interval [CI], 1.00-3.57) and non-Asian race (OR, 3.43; 95% CI, 1.59-7.42) were associated with having an isolate with a matching pattern. Of 375 unique IS6110 patterns among San Francisco isolates, only 9 (2.4%) matched patterns of East Bay isolates. These population-based data suggest that in the San Francisco Bay Area, M. tuberculosis does not rapidly spread across geographic boundaries, and tuberculosis control efforts should focus on transmission within defined areas.