Inspite of the introduction and developments of new molecular diagnostic techniques, the gold standard for mycobacterial diagnosis is still culture. Most of the studies on mycobacteria have been focused on pulmonary infection, while extrapulmonary infection has poorly been explored. AIM To isolate Mycobacteria from extrapulmonary tuberculosis cases by automated and conventional method.SETTING AND DESIGN This study on extra–pulmonary tuberculosis was conducted in the department of Microbiology, Medical College, Kozhikode for a period of one year.MATERIALS AND METHODS A total of 118 specimens were included in the study. History, clinical examination findings and results of relevant investigations were obtained and recorded in a proforma. All specimens were processed by modified Petroff’s method and subjected to smear microscopy. The processed specimens were cultured by both automated and conventional methods.RESULTS Isolation rate by automated method was 14(11.86%) whereas by conventional method it was 4(3.38%). Of total culture positives only 4(3.38%) were smear positive. Isolation from smear negative specimens was 10(8.77%) by automated method and 1(0.87%) by conventional method. HIV– TB co–infection was seen in 15 (12.71%) cases.CONCLUSION Mycobacterial culture and its identification provides a definitive diagnosis of extrapulomary tuberculosis especially in smear negative TB. It also provides isolates for drug sensitivity testing