Bangladesh ranks sixth among higher TB burden countries. Extra-pulmonary TB contributes 12% of all tuberculosis cases in 2008. Risk factors for EPTB in Bangladesh are hypothesized to be different from pulmonary tuberculosis as seen in other high-burden countries. A case control study was conducted to compare the sociodemographic, household condition and lifestyle characteristics between extra pulmonary and pulmonary tuberculosis. This case control study was conducted in thirteen sub districts of Pabna, Shirajgonj and Cox's Bazar districts from January to June 2013. The samples were classified as either extra pulmonary tuberculosis EPTB (cases) or pulmonary tuberculosis PTB (controls). A total of 490 participants including 245 extra pulmonary tuberculosis (cases) and 245 pulmonary tuberculosis (controls), who were being enrolled in DOTS treatment for last six months, were interviewed for epidemiological and clinical information using a standardized questionnaire. Children, adolescent and younger adults had four-time higher risk of being manifested with extra pulmonary tuberculosis [Adjusted odds ratio (AOR) 3.97; 95% Confidence Interval (CI) 1.10 to 14.35] and (AOR 4.50; 95% CI 1.48 to 13.72). Respondents, who lived in their own houses showed three times more chance of getting extra pulmonary disease (AOR 3.11; 95% CI 1.15 to 8.39). Extra pulmonary tuberculosis was seven to eight times more likely to occur among those whose resided in bedrooms ventilated with one (p= .001) or more windows (p =.004) and having window shutter made of glasses or wood slit raised the probability of getting extra pulmonary involvement by twenty times. Households using grain husk and leaves as cooking fuel revealed seven times higher chance of being manifested as extra pulmonary tuberculosis (P <.001). Extra pulmonary cases were three times more common among respondents, who had no history of exposure with known tuberculosis cases than those who had frequent exposure history (AOR 3.01; 95% CI 1.24 to 7.34). Extra pulmonary tuberculosis was found 1.5 times more common among BCG vaccinated respondents than pulmonary tuberculosis (AOR 1.66; 95% CI 1.06 to 2.58). Younger age, house ownership, bedroom ventilation, fuel material used for cooking, contact history and BCG vaccination status might be the important risk factors for the extra pulmonary manifestation of tuberculosis relative to pulmonary tuberculosis.