Background The Eastern Mediterranean Region (EMR) is one of only two WHO regions project to increase tobacco use prevalence by 2025. Evidence shows initiation occurs at an early age, so understanding factors that influence youth tobacco initiation is a high priority. The purpose of this analysis to understand the factors that contribute to youth waterpipe use in the region. Methods This study uses Global Youth Tobacco Survey (GYTS) data from Egypt (2009), Jordan (2009), Kuwait (2009), Lebanon (2010), Morocco (2011), Oman (2010), Saudi Arabia (2010), Tunisia (2010) and Turkey (2012). GYTS is a nationally representative survey of 13-15-year-olds using a standardized protocol. Current cigarette smoking status is defined as having smoked at least once in the last 30 days preceding the survey. Current waterpipe smoking status is defined as use of at least one waterpipe rock) in the last 30 days preceding the survey. Results Of the total sample population, 7.65% were current cigarette smokers, 9.05% current waterpipe smokers, 22.0% experimented with cigarettes, and 26.3% experimented with waterpipe. Across all four countries, girls were more likely than boys to have negative opinions about tobacco use. Male gender and parental smoking were strong predictors of experimentation with both cigarettes and waterpipe when controlling for other variables. In addition, those who believed that waterpipe smoke was not harmful were more likely to experiment with waterpipe (OR=2.32, 95CI%: 1.8-2.9). But no association was seen between smoking behavior and perceptions of harm from cigarette smoke. Apart from Lebanon, over 30% of smokers in each country stated that waterpipe smoking is “not harmful to health”. Conclusions Low perceptions of harm from waterpipe smoking may be an important contributor to youth tobacco use in the EMRO region. Better understanding of attitudes, knowledge and risk behaviors around youth waterpipe smoking can inform effective interventions in these countries.