Abstract Study question Did the values of single- and double-strand sperm DNA breaks (SSB and DSB) increase during the SARS-CoV-2 pandemic? Summary answer During the SARS-CoV-2 pandemic (2020), the mean values of SSB and DSB in infertile patients were statistically higher compared to the periods 2018-2019 and 2021-2022. What is known already Some studies have found lower sperm concentration and motility in patients during and after SARS-CoV-2 infection (COVID-19). These effects appear to be reversible, with significant improvements being observed after three months post-infection (complete spermatogenesis cycle). On the contrary, vaccination against this virus does not seem to affect semen parameters. The objective of the study was to compare the values of SSB and DSB sperm DNA fragmentation in the periods before the pandemic (2018-2019), during (2020, highest number of infections and social confinement), and after (2021-2022, lower infection rate, end of social confinement and vaccination period). Study design, size, duration The average SSB and DSB sperm DNA fragmentation values of 11,215 patients referred from 74 fertility centres throughout Spain from January 2018 to December 2022 were retrospectively compared. Participants/materials, setting, methods Semen samples from infertile patients were analysed using the Comet assay in alkaline or neutral pH conditions to evaluate SSB or DSB, respectively. Three periods were compared (two years before, during 2020, and two years after). Mean SSB and DSB values were statistically compared among these periods using the Kruskal-Wallis and Mann-Whitney tests. Differences were established at the 99% confidence interval. Main results and the role of chance The average SSB values obtained were: 41.67%±15.33 in 2018-2019; 43.92%±17.84 in 2020, and 41.68%±18.58 in 2021-2022. The average DSB values obtained were: 65.64%±14.27 in 2018-2019; 67.77%±13.90 in 2020, and 65.23%±15.18 in 2021-2022. The SSB and DSB values were statistically higher in 2020 compared to the periods 2018-2019 and 2021-2022 (p < 0.001 in both cases). No differences were detected between the previous period (2018-2019) and the following period (2021-2022) (p = 0.101 and p = 0.235, respectively). Limitations, reasons for caution The observed increase in SSB and DSB values during 2020 cannot be directly attributed to the SARS-CoV-2 infection (COVID-19). It is possible that it is associated with other concurrent factors. The studied samples were only from infertile patients, not from the general male population. Wider implications of the findings Given that the SARS-CoV-2 virus still exists in 2021-2022 but the social situation has normalized, the increase in fragmentation observed during 2020 could be more related to other aspects of the pandemic, such as social confinement, stress, among others. Trial registration number Not applicable