Infection by Mycobacterium tuberculosis (MTB) is assumed to be caused by a single strain, and several MTB strains within the same patient are rarely considered. The present study analyzes the phenomenon of mixed infections by MTB in a group of 50 patients with both respiratory and extrarespiratory tuberculosis. First, the proportion of patients with infection by >1 strain was defined, and second, the clonal composition of the MTB populations at different infected sites was studied. In 3 (6%) of 50 patients, >1 strain was cultured, which indicates that mixed infections are not anecdotal. The coinfecting strains were not equally distributed at the respiratory and extrarespiratory site, which reflects a compartmentalization of the infection. In 1 patient, although 2 strains were found at the respiratory site, only 1 of these strains was involved in the extrarespiratory infection, which suggests that clonal selection can occur in the dissemination of the infection.