The aim of the study was to evaluate the diagnostic potential of immunocytochemical staining for the detection of Mycobacterium tuberculosis complex-specific antigen MPT64, in tuberculous lymph node aspirates, cerebrospinal fluid, and effusions from pleura and abdomen. One hundred ninety patients with a diagnosis of tuberculosis (cases) and 80 patients with nontuberculous lesions (controls) were enrolled and differentiated on the basis of clinical features, histology, cytology, clinical biochemistry, Ziehl-Neelsen staining, Lowenstein-Jensen culture, and response to antituberculous therapy. Cervical lymph nodes fine-needle aspirate (n = 150), cerebrospinal fluid (n = 27), pleural fluid (n = 41), and peritoneal fluid (n = 52) were collected and stained with anti-MPT64 and anti-BCG antibodies using immunocytochemistry. Nested-PCR for IS6110 was done for comparison and to calculate the diagnostic indices of the ICC staining. ICC staining with anti-MPT64 was positive in 128/190 (67.4%) tuberculous smears and in 4/80 (5%) control smears thus giving sensitivity of 67.4% and the specificity of 95%, while anti-BCG was positive in 112 (58.9%) tuberculous smears and in 16/80 (20%) control smears with sensitivity of 58.9% and specificity of 80%. When diagnostic validation of ICC was done using PCR as the gold standard, the overall sensitivity, specificity, positive- and negative-predictive values for ICC staining in smears with anti-MPT64 was 96, 96, 95, and 97%, respectively, while the corresponding values for anti-BCG were 87, 88, 86, and 88%. ICC staining using anti-MPT64 represents a robust and simple method for establishing an early etiological diagnosis of M. tuberculosis complex infection in extrapulmonary tuberculosis. Diagn. Cytopathol. 2012. © 2011 Wiley Periodicals, Inc.