The physician and andrologist must turn to semen characteristics to decipher what are the causative agents behind male infertility. WHO standard protocol requires analysis of sperm concentration, motility, and morphology. However, recent evidence implies that such parameters are not enough to fully depict the basis for male infertility and suggests that the effects of sperm DNA damage on infertility be considered. With the increasing ease of artificial reproduction, factors effecting embryo viability and offspring health related to the quality of sperm used and associated integrity of DNA must be strictly analyzed. Male gametes with damaged DNA can transmit genetic defects, lead to pregnancy loss, infant mortality, birth defects, and genetic diseases in the offspring. Furthermore, studies report that more than 80% of the structural de novo chromosome aberrations are of paternal origin. This chapter will begin by reviewing the process of spermatozoal chromatin organization and DNA packaging. Next, DNA damage and the factors causing this damage shall be considered. Subsequently, recognition and detection of this DNA damage will be reviewed followed finally by the effects of this damage and clinical applications encompassing treatment options involving antioxidants.