Standard examination of human semen currently remains a main test for examination of male fertility disorders. Although parameters of sperm quality in fertile men are generally higher than in sterile ones, there is a substantial overlap between the two populations, indicating that other important factors affect fertility, but are not assessed in conventional assay. Currently, tests determining the functional properties of sperm have been intensively developed. This review considers an electron microscopic examination of sperm, which assesses the structure and function of the sperm nuclear, penetration and motor apparatus. The detection of sperm chromatin structure can help to understand the causes of early embryonic malformation. Genetically caused and functional disorders of the structure and function of spermatozoa are discussed. Indications for electron microscopic examination of spermatozoa in fertility disorders are given.