Fifteen percent of reproductive-aged couples worldwide are diagnosed with infertility after a 1-year period of failed conception. With male factor infertility occurring in approximately one-half of these cases, the male factor plays a prominent role. Because male infertility can have multiple causes, the American Urological Association (AUA) recommends a detailed medical and reproductive examination with semen analysis before moving forward with more specific testing. Genetic disorders account for up to 30 percent of infertility cases and consist of two major categories: single gene point mutations or single nucleotide polymorphisms (SNPs) and chromosomal abnormalities. The first step in differentiation of the X and Y chromosome occurred with the acquisition of a testis-determining gene. The use of sequence tagged sites (STS) to detect specific deletions expanded the Y-chromosome map. The Y chromosome, once thought to be a defective or nonfunctional chromosome, encodes multiple genes that are necessary for male phenotypic development and reproduction.