Waterpipe smoking is an ancient method of tobacco smoking practiced worldwide. There is a common belief that waterpipe smoking is a safer alternative to cigarette, but many studies showed that some toxicants were associated with cancer risk, significantly higher in waterpipe smoking. Thus, this study aimed to evaluate the status of waterpipe smoker's buccal cells and its cancer risk using the buccal micronucleus cytome test. Forty waterpipe smokers (noncigarette smokers) were recruited and paired by gender, age and alcoholic habits with 40 control subjects. One-thousand cells from each individual were analysed and the number of pyknotic cells (PYC), karyolitic cells (KYL), karyorrhetic cells (KHC), condensed chromatin (CC), binucleated cells (BN), basal cells (BC), nuclear buds (NBUD) and differentiated cells (DIFF) were counted. Additionally, 2000 differentiated cells were analysed counting micronucleated cells (MNi) and nuclear buds. We observed an increasing P< 0.05 in all waterpipe smoker's cell parameters, except DIFF (fold-decrease). Only CC showed no differences between groups. The interference in the cell cycle plus DNA damage observed in this study could be responsible for the high number of damaged cells and in death process, showing the importance of our study and the high risk in waterpipe smoking.