The incidence of tuberculosis in Estonia has increased from 21.5 in 1991 to 44.6 per 100 000 in 2000. Regardless of the increase in pulmonary tuberculosis, the annual number of incident cases of extrapulmonary tuberculosis (EPTB) during 1991–2000 was stable (around 65 per year). The relative frequency of EPTB decreased from 16.9% in 1991 to 10.1% in 2000. We found significant dissimilarities in the distribution of different localizations of EPTB forms both between the age groups and between the time periods. Bacteriological/ histological confirmation of diagnosis was 60% in tuberculosis pleurisy and 59% in urogenital tuberculosis. For bone-joint tuberculosis the confirmation rate was 10%. Majority of patients with EPTB have only minimal constitutional manifestations. Tuberculin skin test is a potentially useful diagnostic aid in EPTB. Simultaneous pulmonary tuberculosis is a highly valuable diagnostic clue for EPTB, however, such coincidence is relatively uncommon. Since the treatment of tuberculosis, both pulmonary and extrapulmonary, is subject to similar principles, it could be best carried out at departments or centres for tuberculosis. However, management of EPTB often needs collaboration between different specialists in order to settle the issues directly related to the extrapulmonary target organ.