Ejaculated mouse sperm retrieved from the uteri are more susceptible to DNA damage during freeze-drying and freezing without cryoprotection than epididymal sperm. This prompted us to speculate that a factor present in the uterus after mating, either male or female derived, was responsible for increased susceptibility of ejaculated sperm to DNA damage during preservation and that the differences between epididymal and ejaculated mouse sperm in response to stress originated from varying nuclease activity. We first exposed epididymal sperm to the uterine content from females mated to vasectomized males (UCSP), to the uterine content from unmated females in estrus (UC), and to the seminal vesicle fluid (SVF) and examined sperm chromosomes after intracytoplasmic sperm injection (ICSI). We found an increased incidence of chromosome breaks and extremely severe DNA breakage after exposure to UCSP and SVF, respectively, but the chromosomes were normal in sperm exposed to UC. Comet assay results verified that DNA damage after exposure to SVF was present in sperm before fertilization. Next, we examined nuclease activity in sperm and their associated components with a plasmid digestion assay. Nuclease activity was detected in isolated epididymal and ejaculated sperm, as well as in epididymal fluid and seminal plasma, and was much more pronounced in all samples originating from ejaculate. The combined results from the present study imply that there are intrinsic differences between the epididymal and ejaculated mouse sperm preparations in their susceptibility to nuclease-dependent DNA damage that originates from their nuclease activity. This nuclease activity was detected both in the sperm-free fraction of preparations and isolated sperm.