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Introduction Tobacco smoking, common in people living with human immunodeficiency virus (HIV), is associated with increased mortality and morbidity. This study aimed to determine the proportion of current smokers, as well as assess the factors associated with tobacco smoking and drinking alcohol, among people living with HIV (PLHIV) in Nepal. Methods A cross-sectional study was conducted at an antiretroviral therapy (ART) clinic in Kathmandu, Nepal between September and December 2014. Data were collected among 132 HIV infected individuals using a random sampling technique and face-to-face interview. Binary logistic regression analysis was performed to estimate the factors associated with current tobacco smoking and drinking of alcohol. Results Among the HIV infected people, the proportion of current tobacco smoking was 26.5% (95% Confidence Interval (CI): 18.9-34.1), while drinking of alcohol was 22.7% (95% CI: 15.5-30.0). The respondents who were infected with HIV, after sexual contact with sex workers, were more likely to smoke tobacco (OR=15.2, 95% CI: 4.35-53.08) and drink alcohol (OR=4.50, 95% CI: 1.70-11.93) than those who were infected from drug needle use and blood transfusion. HIV infected individuals, who forgot to take ART medication, were three times more likely (OR=3.17, 95% CI: 1.36-7.38) to drink alcohol than those who did not forget to take ART medication. Conclusions Proportion of people who smoke tobacco and drink alcohol is high among the HIV infected individuals who had sexual contact with sex workers in Nepal. There is an urgent need to develop immediate, sustainable and efficient programs to control tobacco smoking and alcohol drinking among vulnerable populations in low and middle-income countries like Nepal.