Denmark is an area of low incidence of HIV and tuberculosis (TB). The number of newly reported cases of HIV has been stable during the 1990s, whereas the number of TB cases has doubled in Denmark in the past decade, mainly due to immigration. However, among native Danes the incidence of TB has increased in the younger age groups, indicating more newly infected persons. This study was performed in order to assess the impact of the HIV epidemic and immigration on TB incidence among native Danes. The study was also designed to reveal transmission patterns of TB among HIV-positive patients. Data from HIV-TB co-infected patients identified in the national registers of TB and AIDS from 1992-95 were collected retrospectively from medical records. Restriction fragment length polymorphism (RFLP) analyses of TB isolates from co-infected patients were compared with all patterns registered in the nationwide Danish RFLP database (approximately 1,700 patients). Sixty-seven co-infected patients were identified, 26 Danes and 41 immigrants, representing only 4% of all TB cases during the study period. Danish co-infected patients were part of a cluster, i.e. they had a RFLP-pattern identical to a pattern in the national RFLP database, more often than immigrants (83% vs. 45%, p < 0.005). In only 2 cases were co-infected Danes and immigrants part of the same cluster. Danish HIV-TB co-infected patients were more often intravenous drug users than were co-infected immigrants (p < 0.0005). In conclusion, we found no evidence to suggest that the increase in TB incidence among young Danes was caused by the HIV-epidemic or transmission from immigrants. TB among HIV-positive Danes is most often due to recent infection. The patients often belong to a subpopulation living in Copenhagen characterized by intravenous drug use.