Comparative studies in primates are extremely restricted because we only have access to a few types of cell lines from non-human apes and to a limited collection of frozen tissues. In order to gain better insight into regulatory processes that underlie variation in complex phenotypes, we must have access to faithful model systems for a wide range of tissues and cell types. To facilitate this, we have generated a panel of fully characterized chimpanzee (Pan troglodytes) and human induced pluripotent stem cell (iPSC) lines derived from fibroblasts of healthy donors. All lines are free of integration from exogenous reprogramming vectors, can be maintained using standard iPSC culture techniques, and have proliferative and differentiation potential similar to human and mouse lines. To begin demonstrating the utility of comparative iPSC panels, we collected RNA-seq data and methylation profiles from the human and chimpanzee iPSCs and their corresponding fibroblast precursors. In order to demonstrate the utility of this panel in studying dynamic developmental processes we collected RNA-seq for a four day time course. We observed conservation of this early developmental period with a reduction of variance shared by both species at the onset of differentiation. In order to determine the fidelity of iPSC derived cell types to a primary tissue, we collected RNA-seq for cardiomyocytes derived from our human and chimpanzee iPSC panel as well as from postmortem heart tissue from both species. We found that while iPSC-derived cardiomyocytes are still in a fetal state, they are able to recapitulate many of the interspecies gene expression differences identified in adult heart tissue,indicating they are a good model to study inter-primate gene regulatory differences. The work contained in this thesis will help realize the potential of iPSCs, and in combination with genomic technologies, transform studies of comparative evolution.