The sex chromosomes play a highly specialized role in germ cell development in mammals, being enriched in genes expressed in the testis and ovary. Sex chromosome abnormalities (e.g., Klinefelter [XXY] and Turner [XO] syndrome) constitute the largest class of chromosome abnormalities and the commonest genetic cause of infertility in humans. Understanding how sex-gene expression is regulated is therefore critical to our understanding of human reproduction. Here, we describe how the expression of sex-linked genes varies during germ cell development; in females, the inactive X chromosome is reactivated before meiosis, whereas in males the X and Y chromosomes are inactivated at this stage. We discuss the epigenetics of sex chromosome inactivation and how this process has influenced the gene content of the mammalian X and Y chromosomes. We also present working models for how perturbations in sex chromosome inactivation or reactivation result in subfertility in the major classes of sex chromosome abnormalities.T he evolution of sex chromosomes from a pair of autosomes is clearly advantageous to species in enabling sexual reproduction and the genetic fitness that results, but also necessitates the coevolution of strategies to deal with unique situations that arise. These include the lack of homology between the X and Y chromosomes in the male germline in which autosomal homologs must pair and the imbalance in Xlinked gene dosage between males and females. In mammals, this sex chromosome imbalance is dealt with by inactivating one of the two X chromosomes during early female development. In the female germline, the inactive X chromosome is reactivated before meiosis. In the male germline, the X and Y chromosomes undergo meiotic inactivation that is linked to their unique unpaired status. This is a conserved process and has important implications for the evolution of sex chromosome gene content. In this article, we will cover these different aspects of sex chromosome behavior and function in mammals, including the role of sex chromosomes in sex determination and the behavior of the sex chromosomes during gametogenetesis, particularly in the male germline.