Scan to discover online Background & Objective: Micronucleus assay of buccal mucosa cells is a simple biomonitoring method for diagnosing the genetic damages of toxic agents. The aim was to study the genotoxic effect of waterpipe smoking on buccal mucosa cells using micronucleus assay. Methods: This was a case control. A total of 30 male waterpipe smokers and 30 non-smokers were included in the study. The exfoliated buccal mucosa cells were scrapped using wooden spatula and were spread over glass slides. The mean number of micronuclei was determined using Feulgen-stained slides. The number of micronuclei per 1000 cells was calculated and compared between the two groups of smokers and non-smokers. Results: The mean number of micronuclei in waterpipe smokers and non-smokers was 1.94±0.39 and 1.68 ± 0.35, respectively. The micronuclei count in waterpipe smokers was significantly higher than non-smokers (P=0). The difference between the number of waterpipe smoking and micronuclei count was significantly different (P=0). Conclusion: The mean number of micronuclei in buccal mucosa cells of waterpipe smokers was significantly higher than non-smokers. The genotoxicity effect of waterpipe was dosedependent.