Inbreeding is known to cause deleterious effects upon reproduction and survival, but its effects upon sperm DNA integrity have not been examined. In the present study, we analyzed this relationship among three endangered ungulates: Gazella cuvieri, Gazella dama mhorr, and Gazella dorcas neglecta. In addition, we examined whether levels of sperm DNA fragmentation are associated with semen quality. The magnitude of sperm DNA damage in the two species with high levels of inbreeding (G. cuvieri and G. dama mhorr) was extremely high when compared to the species with low levels of inbreeding (G. dorcas neglecta) and to values previously reported for outbred populations. Levels of sperm DNA fragmentation significantly increased with inbreeding and age. Increased DNA damage in sperm was associated with increased sperm head abnormalities, lower percentage of sperm with an intact acrosome, and poor motility. Our findings suggest that the link between inbreeding and semen quality is mediated by the effects of inbreeding upon sperm DNA damage. The deleterious effects of inbreeding upon the paternal genome likely decrease male fertility and may cause genetic damage to future generations. Because inbreeding is common among endangered species, high levels of sperm DNA damage may have considerable impact upon the viability of their populations.