Mycobacterium bovis can be an important etiological agent for extrapulmonary (EP) manifestations of tuberculosis, especially in HIV-infected persons. From January 2000 to December 2003, M. bovis as a cause of EP tuberculosis was investigated at the Pneumonology Service, Hospital General de Mexico, Mexico City. Eighty HIV-positive (HIV+) patients and 83 HIV-negative (HIV-) with EP involvement (ganglionar, genitourinary, meningeal, cutaneous, peritoneal, and pericardial) were analyzed using clinical, immunological, bacteriological, histopathological, and molecular biology methods. Mycobacterium species were identified by hsp65-RFLP analysis and species of M. tuberculosis complex isolates by spoligotyping. M. bovis was present in 6 HIV- cases (7.2%; 3 with lymphadenitis and 3 genitourinary) vs 11 in HIV+ cases (13.75%; 7 with lymphadenitis, 3 genitourinary, and 1 meningeal). Favorable response to retroviral and specific M. bovis chemotherapy was observed. Spoligotyping showed a unique profile in each isolate, 16 belonging to BOV1 lineage and 1 to BOV2 lineage. M. bovis is an significant re-emerging cause of EPTB in Mexico. Consumption of unpasteurized dairy products is the most likely source of transmission. Successful treatment depends on the adequate and opportune identification of the agent responsible.