The aim of the study was to determine the prevalence of shisha smoking; its associated factors and awareness among medical students of Karachi, Pakistan following the imposition of nationwide shisha ban. A cross sectional study was conducted among medical students of two medical universities, namely Sindh Medical College and Aga Khan University Karachi, Pakistan from October till December 2014. A total of 422 participants were included. Data was collected via a self-administered questionnaire. The mean age was 21 ± 1.6 years and 229 (54.26 %) were females. Shisha smoking was found to be relatively common among medical students; the prevalence being 21.5 % out of which 73.62 % were males and belonged to a private medical college p value < 0.001. Majority of those who smoked shisha were aware that it contains tobacco (59.34 %), it has no filtration system (42.85 %), it is harmful (91.20 %) and 47.25 % held the opinion that shisha was not any better than cigarettes. It was alarming that majority students were aware of its harmful effects. However, a significant lack of awareness of the legislation against shisha was found among students.