OBJECTIVE Measure the prevalence of smoking among students of health sciences Faculties in Monastir (Tunisia) and identify factors associated with smoking behavior. METHODS A cross-sectional study based on a self-administered questionnaire conducted among students registered in their second, fourth and sixth year at the Faculties of Medicine and Pharmacy in Monastir, in 2013. Smoker was the subject who, at the time of the survey, smoked at least one cigarette per day. Academic difficulties were used to denote any of the following incidents that a student may experience: passing exams at the retake session, revalidating an internship or repeating a school year. A logistic regression analysis was used to identify factors associated with smoking. RESULTS The number of participants was 634 (285 Medical students and 349 Pharmacy students); they were 170 males and 464 females. The prevalence of smoking was 15%; 95% IC [12.1-17.7]. It was nearly five times higher among male compared to female students (35.3%; 95% IC [28.1-42.5]) vs 7.5%; 95% IC [5.1-9.9]); It was also higher among Pharmacy students than among Medical students (18.9%; 95% IC [14.8-23.0]) vs 10.2%; 95% IC [6.7-13.7]). In the multivariate analysis, the Faculty of Pharmacy (ORa=3.081; 95% IC=[1.7-5.7]), the male sex (ORa=6.929; 95% IC [3.9-12.0]) and the academic difficulties (ORa=1.854; 95% IC [1.02-3.38]) were found to be significantly associated with smoking. CONCLUSIONS The level of tobacco use found among Medical and Pharmacy students is alarming. This serious problem has a negative impact on their behavior and can hinder their role model as future health professionals. Greater efforts are needed to develop anti-smoking programs, to educate students and to offer psychological support to deal with school difficulties.