Over recent years, changes of erythrocytic nuclei have been increasingly used to evaluate genotoxic effects of different compounds such as polycyclic aromatic hydrocarbons (benzo-a-pyrene, naphthalene, β-naphthoflavone), heavy metals (cadmium, mercury), textile mill effluent especially in aquatic ecosystem. However, in fish, both micronuclei and erythrocytic nuclear abnormalities also appear spontaneously and their frequency can be seasonally dependent. The aim of the study was to evaluate the frequency of micronuclei (MN), nuclear abnormalities (NA) including vacuolated nuclei (VN) and cytoplasmic vacuoles (CV) in erythrocytes of Balkan whip snake Hierophis gemonensis and establish the level of spontaneous appearance during the annual cycle. Average frequency of NA was 10.89 ± 4.72% while the MN (0.03 ± 0.03%) and VN (0.04 ± 0.08%) were seldom detected. NA significantly positively correlated with MN (r = 0.319; P < 0.05) and VN (r = 0.363; P < 0.05). Appearance of CV did not correlate with other measured parameters and average frequency was 11.06 ± 8.33%. Significant seasonal variation was found in NA appearance with the lowest value in spring and the highest in winter. VN increase was observed in autumn. MN and CV levels varied between seasons but not significantly. Considering the biological cycle, frequency of NA, VN, MN and CV recorded in pre-hibernation/hibernation increased compared to the active phase, but only NA elevation was significant. Although the obtained results showed differences according to sex, statistical analysis of measured parameters showed the same pattern of seasonal variation in both sexes.