Advancement of stem cell therapy is dependent upon the practicality, safety, and efficacy of the cells being evaluated for clinical application. Over the past decade, the need for banked stem cells which are readily available for use at the time of a patient's diagnosis has become apparent. The overall goal of this dissertation research was to compare induced pluripotent stem cells (iPSCs) to bone marrow-derived mesenchymal stem cells (MSCs), first in terms of their ability to be generated from genetically diverse individuals, and then in terms of their immunogenic and immunomodulatory properties for potential allogeneic use. It has previously been demonstrated in mice that genetic background affects the proliferation and differentiation rates of MSCs. The purpose of our first study was to determine if genetic background affects the efficiency of generating iPSCs from mice. Results of this study confirmed that genetic background does affect both the efficiency of generating iPSCs during the early stages of reprogramming as well as the pluripotent stability of the iPSCs during later stages of reprogramming. The results also confirmed the need to understand the immunogenic and immunomodulatory properties of these cells for potential allogeneic application given that it may not be feasible to generate iPSCs from all individuals or to wait for the time that it takes to generate iPSCs and then screen them for safety and efficacy. The purpose of our second study, therefore, was to evaluate the in vitro immunogenic and immunomodulatory properties of murine iPSCs compared to MSCs using modified mixed leukocyte reactions. Our comparisons revealed that iPSCs generated through both lentiviral and piggyBac reprogramming methods had similar immunogenic properties as MSCs, and more potent immunomodulatory effects than MSCs. This information is critical when considering the use of iPSCs in the place of MSCs for both regenerative medicine and transplant medicine. Further studies must be performed, however, in order to determine if iPSCs retain their immunogenic and immunomodulatory properties upon differentiation into specific cell or tissue types. With this knowledge, we then shifted the focus of our third study to the horse, which is a valuable model for the human immune response. The purposes of this study were to immunophenotype MSCs from horses of known MHC haplotype and to compare the immunogenicity of MSCs with differing immunophenotypes, particularly in regards to MHC class II expression, through modified mixed leukocyte reactions. Results of this study demonstrated for the first time the extreme heterogeneity that exists in MHC class II expression by equine MSCs and that MHC class II positive equine MSCs are capable of inciting an immune response in vitro. This knowledge is critical for the treatment of our equine patients as well as for studies using the horse as an animal model for human diseases. Future experiments to determine if we can modulate this MHC class II expression in culture will be of great interest prior to performing in vivo studies to examine the immune response to allogeneic equine MSCs, and ultimately to compare allogeneic equine MSCs to iPSCs both in terms of their immunogenic and immunomodulatory properties as well as their regenerative ability.