Flow cytometry (FCM) has been extensively used to study mammalian sperm in the areas of reproductive toxicology (to monitor effects from environmental, occupational and therapeutic exposures), veterinary science (to preselect the gender of offspring by sorting X- and Y-chromosome-bearing sperm) and clinical andrology (to assess individual fertility potential). Using FCM, a variety of sperm features can now be rapidly measured on a cell-by-cell basis such as sperm count, viability, acrosomal integrity, mitochondrial function and DNA integrity; the last one is involved in postfertilization failure and embryo toxicity. It is foreseen that only a multiplex approach, which includes FCM assays together with the new genomics/proteomics methods, could increase the predictive power of fertility status and help identify susceptible subpopulations of men at risk for infertility, spontaneous abortions and birth defects.