INTRODUCTION Waterpipe tobacco smoking (WTS) continues to be very common in the Eastern Mediterranean Region (EMR), partially because of cultural acceptance but also because of misconceptions of its harm. This paper aimed to describe the beliefs towards waterpipe harm of university students who smoked waterpipe in five EMR countries. METHODS This study was conducted in 2016 across five EMR countries: Egypt, Jordan, Occupied Palestinian Territories, Oman and United Arab Emirates (UAE). Participants were recruited from among university students in each country. Students’ characteristics, smoking behavior, flavor preference and knowledge of WTS harm were collected using an internet-based survey. Participants were included if they were ever waterpipe tobacco smokers and between 18 and 29 years of age. Bivariate analyses assessed variations in student-perceived WTS harm across the countries. Linear regression analysis was used to assess WTS perceived harm differences between students in the different countries. RESULTS A total of 2 544 university students participated from the five countries. Among ever smoking students, 66% reported WTS in the past 30 days, with the highest proportions (40%) from Occupied Palestinian Territories (OPT) and (41%) Jordan. Dual smoking of waterpipe and cigarettes was highest among students from Egypt. Most participants from the five countries had high level of perceived harm related to WTS during pregnancy. Less than 50% of the students believed that WTS could lead to the death of the smoker, can be harmful for non-smokers and have an addictive effect. Female students, those older than 22 years, and those who didn’t smoke waterpipe in the last 30 days significantly had a higher level of WTS perceived harm. Participating students believed that cigarettes are more addictive and contain more nicotine compared to waterpipe. CONCLUSIONS Misperceptions of waterpipe harm are common among university students in the five EMR countries. Immediate public health action is needed, including enforcement of waterpipe tobacco control regulations along with awareness campaigns.