Patients with HIV infection have atypical clinical features of pulmonary tuberculosis; however, our knowledge on how malnutrition affects the clinical presentation is limited. We studied the influence of malnutrition and HIV infection on the clinical and radiological features of pulmonary tuberculosis (TB). We studied 239 consecutive acid fast bacillus-positive adult patients. Patients were investigated by clinical, radiological, anthropometric and laboratory methods. 78% of the patients were malnourished (BMI < 18.5) and 43% were severely malnourished (BMI < 16). 20% were HIV-positive. HIV-positive TB had significantly more oral candidiasis (OR = 3.72), diarrhoea (OR = 2.71), generalized lymphadenopathy (OR = 2.63), skin disorders (OR = 2.27), neuropsychiatric illness (OR = 2.44), hilar lymphadenopathy (OR = 2.07), but less cavitation (OR = 0.64) and upper lung lobe involvement (OR = 0.70). HIV-negative and severe malnourished patients presented more often with dyspnoea (OR = 1.44), diarrhoea (OR = 1.64), night sweat (OR = 1.83), and less with haemoptysis (OR = 0.58) and cavitation (OR = 0.64). The size of Mantoux was associated with HIV infection and malnutrition. In a logistic regression analysis both HIV status and malnutrition were associated with atypical presentation of pulmonary tuberculosis. Malnutrition and HIV infection both contribute for atypical presentation of pulmonary tuberculosis. The risk of such atypical presentation is particularly high among the severely malnourished HIV-infected patients.