The occurrence of DNA fragmentation in mammalian spermatozoa was identified in 1993. In human, sperm DNA fragmentation is particularly relevant in subfertile patients (i.e, those subjects more likely to be treated by assisted reproductive techniques). Thus, concerns have been raised about the possibility that sperm with DNA fragmentation may be involved in the process of fertilization, in particular when invasive techniques (such as intracytoplasmatic sperm injection) are applied. Knowledge of the mechanisms responsible for generation of DNA strand breaks may thus help in disclosing and possibly identifying new therapies for the treatment of male infertility. However, the mechanisms involved in generating sperm DNA anomalies are far from being clarified. In this review, we summarize and critically analyze the main current theories that explain generation of DNA fragmentation in spermatozoa: abortive apoptosis (anomalies in apoptosis that occur normally during spermatogenesis), problems in packaging of chromatin (mainly anomalies in histone to protamine substitution) and generation of reactive oxygen species (that may occur at any level during spermatogenesis, sperm maturation and transit in the male genital tract).