Background: The aim of the study was to determine the prevalence of shisha smoking and associated factors among medical students in Malaysia. Materials and Methods: A cross-sectional study was conducted at the Management and Science University from December 2011 until March 2012. The questionnaire consisted of five sections including socio-demographic, social environment, knowledge about shisha, psychosocial factors, and personal shisha smoking behavior. Obtained data were analyzed using Statistical Package for the Social Sciences (SPSS 13). T-test was used to determine the relationships between shisha smoking and socio-demographic characteristic. Results: A total number of 300 medical students participated in this study. Mean age was $22.5{pm}2.5$ years. The majority were female, Malay, single, from urban areas (67%, 54%, 97%, 73%; respectively). The prevalence of shisha smoking among medical students was found to be 20%. The study revealed that many students believed that shisha does not contains nicotine, carbon monoxide, does not lead to lung cancer, dental problems and does not lead to cardiovascular diseases (25%, 20.7%, 22.3%, 29%, 26.7%; respectively). Age and sex were found to be significantly associated with smoking shisha status among medical students (p=0.029, p<0.001; respectively). Furthermore, having parents, siblings and friends smokers of shisha were found to be significantly associated with shisha smoking status (p<0.001, p<0.001, p<0.001; respectively). Furthermore, family problems, problems with friends, financial problems and university life were found to significantly associated with shisha smoking status among medical students (p<0.001, p=0.002, p<0.001, p=0.002; respectively). Conclusions: There is a high prevalence of shisha smoking and a poor knowledge about its impact on health among medical students. More attention is needed to focus on medical education in this regard. The policies that are currently employed in order to reduce the cigarettes smoking should be applied to shisha smoking and shisha products.