AIM: To study and compare the genotoxic effects of tobacco using micronuclei count in individuals with different tobacco-related habits. MATERIALS AND METHODS: A cross-sectional study was done comprising 200 individuals, divided into four groups. Group I: 50 subjects with history of tobacco chewing, group II: 50 subjects with a history of smoking tobacco, group III: 50 subjects with a history of both tobacco chewing and smoking, and group IV: 50 subjects without any habits as controls (age-matched). The study groups were individually further divided into three subgroups which comprised of subjects with history of substance abuse for less than 5, 5 to 10, and greater than 10 years. Exfoliated cells from the buccal mucosa of the subjects were collected and stained using Giemsa stain. A total of 1,000 cells were examined for each case and micronuclei frequency was scored according to the guidelines given by Tolbert et al. Results: The mean number of micronuclei count was 18.28 ± 10.0 in group I (smokeless tobacco users), 11.38 ± 6.3 in group II (subjects with history of tobacco smoking), 22.44 ± 9.8 in group III (subjects with history of using both smokeless and smokable form of tobacco), and 4.86 ± 2.4 in the control group. The statistical difference was found to be highly significant (p < 0.001). Similarly, based on the duration, highly significant difference was notable in the mean number of micronuclei in subjects who had a history of substance abuse for more than 10 years. CONCLUSION: A significantly higher micronucleus frequency was found in smokeless tobacco users than in smokers and controls. Micronuclei assay in the exfoliated buccal cells is a useful and minimally invasive method for monitoring early genotoxic damage. CLINICAL SIGNIFICANCE: Micronuclei assay can be used to detect genotoxic damage at the earliest and, if intervened at this point, may prevent frank malignancy, morbidity, and mortality.