The presence of micronuclei in oral epithelial cells is considered a marker of genotoxicity, which can be identified using exfoliative cytology. The aim of this study was to investigate cytotoxic damage through the evaluation of micronuclei in the oral mucosa of smokers and e-cigarette users compared to nonsmokers. We obtained smears from the buccal mucosa of 68 participants divided in 3 groups (smokers, e-cigarette users and nonsmokers), which were further processed with Papanicolaou stain. The frequencies of micronuclei and micronucleated cells were recorded and statistically analyzed at a level of significance of p < 0.05. The mean micronuclei values per 1000 cells were 3.6 ± 1.08 for smokers, 3.21 ± 1.12 for e-cigarette users and 1.95 ± 1.05 for nonsmokers. The mean values of micronucleated cells per 1000 cells were 2.48 ± 0.91 for smokers, 2.39 ± 1.07 for e-cigarette users and 1.4 ± 0.68 for nonsmokers. Smokers and e-cigarette users had significantly higher values of micronuclei and micronucleated cells compared to nonsmokers, but there were no significant differences between smokers and e-cigarette users. We concluded that the micronuclei count can be used as an early indicator for alterations of oral mucosa and exfoliative cytology represents an accessible tool which could be applied for mass screening.