We investigated tuberculosis transmission during a nine-year period (1988-1996) in a countrywide community-based cohort of HIV-infected persons in Switzerland (the Swiss HIV Cohort Study [SHCS]). We estimated the proportion of tuberculosis cases due to reinfection and relapse, and assessed factors which may increase the risk of tuberculosis transmission. HIV-infected persons were followed prospectively and molecular fingerprinting with insertion sequence (IS) 6110, 36-bp direct repeat, and IS6110-PCR was used to determine M. tuberculosis case clustering. Out of 7999 SHCS participants, 267 persons developed tuberculosis. 158 M. tuberculosis isolates from 138 patients were available for study. Molecular analysis identified 33 (24%) episodes of tuberculosis associated with 12 clusters including 2 to 8 patients. Two patients experienced reinfection, and nine had a relapse. Detailed contact investigation identified definite or possible epidemiological links between 21 of 33 cluster patients (64%). Multivariate logistic regression analysis did not identify any risk marker significantly associated with clustering. During a nine-year period, one fourth of tuberculosis cases were grouped in clusters within a selection of 138 HIV-infected patients. This may represent the lowest estimation of recently acquired tuberculosis infection. There were no large institutional or community outbreaks among HIV-infected participants of the Swiss HIV Cohort Study.