For centuries, tuberculosis has been identified as a burden to seafarers. In this study, we assessed the magnitude of tuberculosis among merchant seafarers today. Furthermore, we identified the most likely routes of M. tuberculosis transmission by the use of DNA fingerprinting. A database containing all culture-positive tuberculosis cases in Denmark in 1992-2003 was combined with a register on all seafarers and their employment periods aboard Danish ships. All strains of M. tuberculosis were analysed using DNA-subtyping. 64 cases of culture positive tuberculosis among seafarers were identified. The risk of tuberculosis among males was 1.51 (1.10-2.01) compared with the general population. Two of the 64 cases were likely to be shipping-related, 5 were possibly shipping-related, and 10 were less likely to be shipping-related. The remaining 47 cases were very unlikely to be shipping related. Including the 2 first categories, the incidence was 0.09 cases per 1000 y at sea. The excess risk of tuberculosis among active and former Danish seafarers is most probably due to infections acquired in Denmark. Despite multi-cultural crews aboard, including many from high-incidence countries, our study indicates that only limited transmission of M. tuberculosis takes place among crew aboard modern ships or during shore leaves.