SETTING: Denmark, a high-income country with a low prevalence of tuberculosis. OBJECTIVE AND DESIGN: Molecular epidemiological studies of Mycobacterium tuberculosis strains are conducted worldwide, and distinct strains have been associated with large outbreaks of tuberculosis. This is the first systematic population-based search for distinct strains of M. tuberculosis in Denmark among 4102 strains DNA fingerprinted nationwide from 1992 to 2001. RESULTS: A specific strain of M. tuberculosis has emerged rapidly in Denmark: in 1992, the Danish Cluster 2 strain accounted for 5.8% of all culture-positive Danish-born cases, increasing to 29.0% in 2001. The Cluster 2 cases were on average younger (41.8 vs. 51.4 years), more likely to be male (81.4% vs. 64.1%), and more likely to have pulmonary involvement only (90.3% vs. 64.6%) than other Danish-born cases. During the first 4 observation years, they were mainly found in the capital city, Copenhagen, but were later increasingly observed in the provinces. CONCLUSION: The reasons for the increasing dominance and change in geographical distribution of Cluster 2 strains in Denmark is unknown, but may be partly explained by the fact that Cluster 2 is associated with younger males with pulmonary disease manifestation. We consider it as an outbreak and believe the situation requires increased focus on early tuberculosis diagnosis and control of transmission in Denmark.