The sperm chromatin structure assay (SCSA) was introduced by as a method to determine the susceptibility of sperm DNA to denaturation and how those results related to fertility. This initial study used human sperm and was followed by studies in bulls and boars . This assay was one of the first to introduce the technique of flow cytometry, which has the ability to evaluate specific sperm compartments of large numbers of sperm in a short time, as a methodology to evaluate sperm quality and further define the relationship of sperm quality to fertility. For any assay to be of use clinically, it must not only be validated and adapted for the species of interest, but guidelines that associate specific levels of fertility with assay results must be defined. This review will describe how our laboratory uses the SCSA for clinical diagnosis of reduced fertility in the stallion.