Reactive oxygen species (ROS) have been implicated in many pathologies, including sub- and infertility. Freeze/thawing of sperm samples is routinely performed in the cattle breeding industries in order to perform artificial insemination. This freeze/thaw procedure is known to induce ROS in sperm samples. Lipid peroxidation in fresh and frozen/thawed sperm cells was assessed by mass spectrometric analysis of the main endogenous phospholipid class, phosphatidylcholine, and by fluorescence techniques using the lipid peroxidation reporter probe C11-BODIPY(581/591). Peroxidation as reported by the fluorescent probe, clearly corresponded with the presence of hydroxy- and hydroperoxyphosphatidylcholine in the sperm membranes, which are early stage products of lipid peroxidation. This allowed us, for the first time, to correlate endogenous lipid peroxidation with localization of this process in living sperm cells. Lipid peroxidation was particularly strong in the midpiece and tail of frozen/thawed spermatozoa and significantly less intense in the head. Induction of peroxidation in fresh sperm cells with the lipid soluble ROS tert-butylhydroperoxide gave an even more pronounced effect, demonstrating antioxidant activity in the head of fresh sperm cells. Furthermore, we were able to show that spontaneous peroxidation was not a result of cell death, as only a pronounced subpopulation of living cells showed peroxidation after freeze/thawing.