The global burden of childhood pulmonary TB has been underappreciated, in part due to difficulties in obtaining microbiological confirmation of disease. Most HIV-uninfected children can be diagnosed using a combination of clinical and epidemiological features, tuberculin skin testing and chest radiography, as represented in different scoring systems. However, accurate microbiologic diagnosis has become increasingly important for timely use of effective treatment. Mycobacterial culture confirms the diagnosis of TB and provides drug susceptibility data but is not available in most areas with a high TB prevalence. Moreover, culture has poor sensitivity in children who usually have paucibacillary disease. The HIV epidemic has made definitive diagnosis even more challenging due to nonspecific clinical and radiological signs. In high HIV-prevalence areas, scoring systems have been especially variable, lacking sensitivity and specificity. Newer methods for diagnosis are aimed either at detecting the organism or a specific host immune response. Methods for organism detection have focused on collection of better samples, improved culture techniques, molecular methods or antigen detection. Recent advances include the use of sputum induction for obtaining a more reliable specimen, faster and more sensitive culture methods, and rapid detection of the organism and drug resistance based on nucleic acid amplification. Improved methods for detecting a specific host response have largely focused on the use of IFN-g release assays. Even with newer methods, accurately diagnosing childhood TB may be challenging. Greater efforts to obtain a microbiologic diagnosis should be made in children, even in primary care settings. Further research to develop a more accurate, cost-effective and simple diagnostic test for childhood TB is urgently needed.