Introduction Coronavirus disease 2019 (COVID-19) is characterized by impact on different systems of human body. Recently, several anti-COVID vaccines have been developed. Material and methods In our study, we included two groups of males: GROUP1, anti-COVID vaccinated males, n = 46, and GROUP2, n = 43, non-vaccinated males, who all fell ill with the Coronavirus infection. A level of semen DNA fragmentation was characterized by Sperm DNA Fragmentation Index (SDFI) that was calculated before infection and compared with data at every month after laboratory recovery. The Mann–Whitney test was used to establish differences between parameters, with p <0.05 considered significant. Results Compared with the pre-COVID baseline we registered significant increasing of SDFI in each group of participants: 35.3 ±4.7% vs 18.6 ±5.8% in GROUP1, p = 0.0009, and 41.8 ±5.6% vs 19.2 ±6.1% in GROUP2, p = 0.0006. At the 2nd month after recovery SDFI in GROUP1 and GROUP2 continued to grow and reached its peak to 40.6 ±6.4% and 49.7 ±7.2% respectively. Thereafter SDF indexes in both Groups started to decrease, normalizing at the 7th month after COVID-19 recovery in GROUP1 and at the 9th month in GROUP2. Conclusions COVID-19 causes a gradual increase in semen DNA fragmentation, which peaks at the 2nd month after recovery and is more pronounced in unvaccinated men. Normalization of SDFI occurs no earlier than at the 7th month in vaccinated and at the 9th month in non-vaccinated men.