To determine a detailed picture of tuberculosis (TB) epidemiology in Hamburg, Germany, 423 Mycobacterium tuberculosis complex isolates from 77.0% of all patients with culture-confirmed TB diagnosed from 1997 to 1999 in Hamburg were analyzed by IS6110 DNA fingerprinting. IS6110 restriction fragment length polymorphism (RFLP) clusters were assumed to have arisen from recent transmission. Results of contact tracing and additional patient interviews were used for further epidemiological analyses. Of the 423 cases, 398 were included in the cluster analysis, of which 135 (33.9%) were classified into 35 clusters ranging from 2 to 23 patients. Epidemiological links verifying recent transmission could be confirmed for 87 of the 135 clustered patients. Risk factors for recent transmission were calculated by a two-step procedure: first, based on patients with clustered isolates; and second, based on patients with clustered isolates and transmission links. In both analyses, alcohol abuse appeared to be the strongest predictor for recent transmission, followed by a history of previous contact tracing and unemployment. Homelessness, foreign ethnicity, sex, drug addiction, and human immunodeficiency virus positivity were not independent risk factors for clustering in multivariate analyses. Classical contact tracing performed prior to IS6110 RFLP analysis identified only 24 of the 135 clustered patient. In conclusion, recent transmission seems to be frequent in Hamburg and was found to be strongly associated with alcohol abuse. Conventional contact tracing appears to be insufficient for the detection of recent transmission chains. The data presented also indicate that improved TB control strategies, including the use of RFLP for the detection of transmission chains, are needed for TB control in the setting of countries with a low incidence of TB.