A fluorescent assay was used to reveal the presence of lipid peroxidation (LPO) in spermatozoa from individuals with genitourinary infections (GI). The incidence of LPO was compared with sperm pathologies (apoptosis, immaturity, necrosis) evaluated by transmission electron microscopy (TEM) and motility. A C11-BODIPY 581/591 probe was used to detect and localize LPO in sperm from 34 individuals. The sperm morphological characteristics were studied by TEM and the results were mathematically assessed. Using the LPO percentage we divided the patients into four groups. Group 1 included ten patients with GI with almost normal progressive motility, a very low percentage of LPO and sperm pathology values that were not far from the standard ranges. Group 2 had eleven infected patients showing reduced motility, LPO of 10 to 20% and sperm pathologies that were just out of normal range. Group 3 included 6 infected patients with progressive motility r22%, low levels of LPO with a higher percentage of apoptosis and necrosis. Group 4 had 7 patients showing normal semen parameters, without GI, LPO ranged from 0% to 1% and a normal incidence of sperm pathologies. In all groups, LPO was inversely correlated with sperm motility and directly correlated with low semen quality. However, the LPO percentage was low in Group 3, in which sperm necrosis, concomitant with GI, was the predominant pathology. C11-BODIPY 581/591 is a useful labeling method for quantifying and localizing LPO in spermatozoa from patients with GI. The detection of LPO could be questionable in cases of sperm necrosis because in this pathology the plasma membrane is often disrupted and the lipidic probe is unable to intercalate within the phospholipidic bilayer.