Fertilization, the fusion of male and female gametes, is an incompletely known, multistep, complex process, in which many factors participate. Fertilization is a precisely regulated, species-specific process, but some cellular mechanisms are similar for many mammal species. The studies of mechanisms of male and female gamete production enable understanding of fertilization issues and, as a result, make the analysis of the causes of infertility possible. Male and female infertility is a progressive phenomenon. The development of laboratory medicine enables the analysis of molecular aspects of the reactions between gametes, which may result in better diagnosis of many infertility cases and indicate the direction of therapeutic management. The fertilization process is accompanied by many biochemical reactions, in which glycoproteins present in human ejaculate play a very important role. Glycan structures enable glycoproteins to participate in the interactions between cells, including those between gametes. The analysis of the glycosylation profile and degree of ejaculate glycoproteins not only contributes to deepening the knowledge about mechanisms accompanying the fertilization process, but also may be useful as an additional diagnostic marker of male infertility. The aim of the present review is to approach selected molecular mechanisms occurring in the male genital tract, related to the fertilization process, as well as to analyze their influence on male fertility.