Background: Asthma is a chronic inflammatory disease commonly managed using salbutamol inhalers. Prolonged exposure to inhaled medications may induce genotoxic alterations, including micronucleus (MN) formation in buccal epithelial cells. Limited data exist regarding such effects among Sudanese asthmatic patients. Objective: To assess the frequency of micronuclei in buccal mucosa among asthmatic patients using salbutamol inhalers and compare the findings with healthy controls in Shendi City. Methods: A descriptive comparative cross-sectional study was conducted on 100 participants: 50 asthmatic patients using salbutamol inhalers and 50 age- and sex-matched healthy controls. Buccal smears were collected, fixed with 95% ethanol, and stained using the Papanicolaou technique. Micronuclei were examined microscopically, and data were analyzed using SPSS employing Chi-square and ANOVA tests. Results: Micronucleus positivity was detected in all asthmatic patients (100%) compared with 80% among controls (p = 0.000). MN frequency increased significantly with age group 20–40 years (52%, p = 0.026) and with duration of inhaler use (p = 0.000). No significant association was found between MN frequency and gender (p = 0.072). Conclusion: Long-term use of salbutamol inhalers is associated with a significant increase in micronucleus frequency in buccal epithelial cells, suggesting potential genotoxic effects. Further studies using DNA-specific stains, such as Feulgen, are recommended to validate these findings.