Cytotoxic therapies are widely used to treat malignant and non-malignant conditions, but they can exert adverse effects on the male germline. Spermatogenic cells are particularly vulnerable to these treatments due to their high proliferative activity and reduced capacity for DNA repair. Current evidence indicates that cytotoxic agents can induce molecular alterations in spermatozoa, affecting both the genome and the epigenome. At the genomic level, increased sperm DNA fragmentation, chromosomal abnormalities and, in some cases, stable sequence mutations have been observed, with variable persistence depending on treatment intensity and individual susceptibility. At the epigenetic level, cytotoxic exposures can disrupt DNA methylation patterns and alter the profile of microRNAs, a class of small non-coding RNAs crucial for spermatogenesis, fertilization, and early embryogenesis. Although only limited human data are available, studies indicate that persistent sperm epimutations may remain detectable long after treatment, raising concerns about potential impacts on offspring and, theoretically, transgenerational inheritance. Traditional parameters such as semen analysis and hormonal profiles are insufficient to detect these molecular alterations. Therefore, DNA integrity, DNA methylation signatures, and sperm-borne miRNAs are emerging as promising biomarkers for monitoring reproductive function following cytotoxic exposure. Fertility counselling, in particular semen cryopreservation prior to treatment, remains an essential component of clinical management.