It is well established that biological sex affects risk, age-of-onset, and/or severity of many psychiatric and neurological diseases. Men have a higher incidence of Parkinson's disease, autism, and schizophrenia while women show a higher incidence of major depressive disorder, anxiety disorder, Alzheimer's disease and multiple sclerosis. Additionally, researchers have observed sex differences across nervous system properties related to neurogenesis, morphology, gene expression, synapse density, and connectivity. These differences could be due to differential genetics (XX vs XY), hormonal influence, and/or the complex effects of social environment. To understand the specific factors influencing both disease and “normal” brain function, it is critical to understand the cell and molecular bases of this variation between individuals. In spite of some compelling animal model work, studies analyzing the cell and molecular bases of sex differences in the human brain have, until very recently, been rare. Part of the reason for this is the lack of a human cellular model system for neuroscience that is both biologically relevant and genetically controlled. Here, we propose to establish a well controlled, defined, and manipulatable human stem cell model for studying the impact of genetic sex on cellular mechanisms underlying neuropsychiatric diseases. The system proposed would provide us and others a facile “plug-in” system for adding a sex differences component to stem cell-based analyses. In Aim 1, we propose to develop XX and XY stem cell lines that are fully isogenic outside of the sex chromosome complement. Sex differences cannot be definitively attributed to genetics as long as the autosomal genome also is also divergent, and since there is no natural occurrence of an autosomally isogenic male/female pair, we propose here to engineer human stem cell lines that are genetically identical with the exception of the sex chromosome complement. We will use a Klinefelter embryonic stem cell line (XXY) that we have in hand and develop new iPSCs from Klinefelter fibroblasts. We then will induce these lines to lose either a single X or Y chromosome, creating subclones of autosomally male and female stem cell lines. In Aim 2, we will use the autosomally isogenic stem cell system developed in SA1 to identify genes and proteins that are differentially affected by genetic sex. For this aim we will differentiate our isogenic XX and XY stem cells individually into neurons of the hypothalamus and of the cortex, astrocytes, and microglia and assay differential effects between XY and XX cells on gene and protein regulation.