Abstract Background Weight misperception is the discordance between an individual’s actual weight status and the perception of his/her weight. It is a common problem in the youth population as enumerated by many international studies. However data from Pakistan in this area is deficient. Methods A multi-center cross-sectional survey was carried out in undergraduate university students of Karachi between the ages of 15–24. Participants were questioned regarding their perception of being thin, normal or fat and it was compared with their Body Mass Index (BMI). Measurements of height and weight were taken for this purpose and BMI was categorized using Asian cut offs. Weight misperception was identified when the self-perceived weight (average, fat, thin) did not match the calculated BMI distribution. Chi square tests and logistic regression tests were applied to show associations of misperception and types of misperception (overestimation, underestimation) with independent variables like age, gender, type of university and faculties. P-value of