Technical Abstract: Andrology is one of few fields of medicine and biology in which biochemical and molecular tools are not routinely used for sample evaluation. Consequently, it is highly desirable to develop methods for accurate semen analysis and estimation of current fertility and future fertility in large farm animals including bulls, boars, and stallions. Toward this goal, we have been working on the identification of 'negative' sperm quality markers, i.e. proteins associated with morphologically and/or functionally defective spermatozoa in male farm animals and humans. Ubiquitin, a universal chaperone protein, marks other proteins for degradation by multi-subunit protease, the proteasome. We have discovered that ubiquitin binds selectively to the surface of defective bull spermatozoa during sperm maturation and passage through epididymis. Consequently, ubiquitinated defective spermatozoa can be detected in bull semen samples by various immunological and immunocytochemical techniques which provide an objective, quantifiable marker of bull sperm quality. Further, to the utility of ubiquitin as a 'negative' sperm/semen quality marker, increased bull sperm ubiquitin levels correlate negatively with bulls' fertility. Such a relationship was documented by comparing sperm ubiquitin levels with reproductive efficiency in artificial insemination as well as parentage from natural breeding in a two-sire pasture system. Ubiquitin-based sperm quality assays are relatively easy and not costly to perform and have a number of advantages over other methods of semen evaluation including objectivity, independence from semen handling and storage methods, and universality with regard to recognizing multiple types of obvious and cryptic sperm defects. Further effort will be focused on validation of such assays and their dissemination of artificial insemination and natural breeding programs.