Aim The main purpose of this study was to assess the genotoxic and cytotoxic effect of fissure sealants on buccal epithelial cells. Material and methods The study was conducted on 45 patients (27 girls and 18 boys), seven to 16 years of age (age mean 12.09 ± 2.20). Buccal swabs were collected before (T0), seven (T1), 30 (T2) and 90 days (T3) consequently after fissure sealant placement (Helioseal F®, Equia Fil®, Constic®). Patients or legal guardians filled in the questionnaire regarding the demographic data (age, gender), dietary habits, health status, medication usage, and recent X-ray exposure. DNA damage was analyzed using the micronucleus test. Results Statistically significant difference in the number of buccal cells with condensed chromatin was found between T0 (time before fissure sealant placement) and T3 (90 days after fissure sealant placement) period for Helioseal F® (P = 0.025). For the other two analyzed materials, no difference was observed during the tested period. There was no difference between materials in the same sampling time. Conclusion Apart from an increase in cells with condensed chromatin 90 days after the placement of Helioseal F®, no other nuclear abnormalities were observed for tested fissure sealants. Although these sealants have now largely been used, it is of high importance that their biocompatibility is checked continuously, especially in in vivo clinical studies.