This chapter reviews the clinical significance of sperm chromatin abnormalities, oxidative stress (OS), apoptosis, and microwave hazards for male gametes highlighting the laboratory methods available to assess these aspects of sperm structure and function. DNA fragmentation is particularly frequent in the ejaculates of subfertile men. Assays for detection of sperm nuclear DNA damage can be divided into three groups: sperm chromatin structural probes, tests for direct assessment of sperm DNA fragmentation, and sperm nuclear matrix assays. To accurately quantify OS, levels of reactive oxygen species (ROS) and antioxidants should be measured in fresh samples. Direct methods such as pulse radiolysis and electron-spin resonance spectroscopy have been useful for other systems of the body. Magnetic-activated cell sorting (MACS) using annexin V-conjugated super paramagnetic microbeads can effectively separate non-apoptotic spermatozoa from those with deteriorated plasma membranes based on the externalization of Phosphatidylserine (PS).