Male infertility has traditionally been diagnosed by microscopic assessment of concentration, motility and morphology of sperm in the ejaculate. Most laboratories use sperm isolated by various methods such as density gradient centrifugation to enrich for subpopulations of sperm believed to have greater fertilization potential. These tests are essential to provide the fundamental information on which clinicians base their initial diagnosis. However, in the clinical setting, tests with superior prognostic value are needed. Tests showing much promise are those determining sperm DNA integrity, particularly the Comet, TUNEL, and Sperm Chromatin Structure assays. Sperm nuclear DNA fragmentation has been positively correlated with lower fertilization rates in IVF, impaired implantation rates, an increased incidence of abortion and disease in offspring, including childhood cancer. The mitochondrial genome of sperm has also been shown to be a sensitive marker of sperm health. Although the usefulness of these tests is recognized, insufficient resources have been available to develop standardized tests and protocols that could lead to universally accepted clinical thresholds. Associated with the lack of useful prognostic tests is the lack of improvement in assisted conception success rates despite thirty years of worldwide use. International collaborations should be initiated to develop agreed protocols and establish clinical thresholds.