Proteomics is a research area that has developed rapidly in the last decade. It studies the large-scale characterization of the full protein components of a cell, a tissue, or a biological fluid. In the last decade, clinical proteomics has developed new technology and bioinformatics useful in identifying molecular markers of pathology; the next decade might be the era of proteomics. Seminal plasma (SP) represents a good sample for proteomic analysis in the evaluation of male fertility/infertility. SP is an acellular fluid conglomerate, comprised of contributions from the epididymis and accessory sexual glands. Human SP contains many proteins that are important to the successful fertilization of the oocyte by the spermatozoa. Proteomic studies have identified numerous seminal-specific proteins, and recent reports have provided a further understanding of their function with respect to male fertility. Upon further validation, these proteins may be useful in the clinical distinction between fertility and infertility. This article reviews the proteomic methods, such as one dimensional polyacrylamide gel electrophoresis (1D-PAGE), two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), and mass spectrometry (MS), employed to detect human SP markers involved in fertility and infertility. As such, proteomic studies will help the development of new techniques to identify novel biomarkers for a better clinical diagnosis and treatment of male infertility.