The most obvious difference between the sexes’ genomes is the presence of the Y-chromosome. Although most of Y-chromosome research to date primarily focuses on its role in sex determination and spermatogenesis (fertility), the advancement of molecular genetic tools has provided preliminary evidence that the Y-chromosome is involved in more than just sex determination and fertility. For example, the Y-chromosome has retained genes over evolution that are broadly expressed, dosage-sensitive, and encode proteins involved in chromatin modification, transcription, splicing, and translation. While a thorough discussion of the role of the Y-chromosome outside of the reproductive tract is beyond the scope of this commentary, we direct the reader to a review by Hughes and Page [7] that provides a compelling argument for why we should study the role of the Y-chromosome in the genetics of disease.