A novel application of Hidden Markov Models is used to help research intended to test the immunuregulatory effects of mesenchymal stem cells in a cynomolgus monkey model of islet transplantation. The Hidden Markov Model, an unsupervised learning data mining technique, is used to automatically determine the postoperative day (POD) corresponding to a decrease of graft function, a possible sign of transplant rejection, on nonhuman primates after isolated islet cell transplant. Currently, decrease of graft function is being determined solely on experts' judgment. Further, information gathered from the evaluation of constructed Hidden Markov Models is used as part of a clustering method to aggregate the nonhuman subjects into groups or clusters with the objective of finding similarities that could potentially help predict the health outcome of subjects undergoing postoperative care. Results on expert labelled data show the HMM to be accurate 60% of the time. Clusters based on the HMMs further suggest a possible correspondence between donor haplotypes matching and loss of function outcomes.