The Sperm Chromatin Structure Assay (SCSA) serves as a tool for measuring clinically important properties of sperm nuclear chromatin integrity. The assay utilizes the metachromatic features of Acridine Orange (AO), a DNA probe, and the principles of flow cytometry (FCM). SCSA data are not well correlated with classical sperm quality parameters and have been solidly shown to predict sub/infertility. This assay is ideally suited to human and animal fertility clinics to assess male sperm DNA integrity as related to fertility potential and embryo development as well as effects of reproductive toxicants. A detailed description of the SCSA follows.