Graft versus host disease (GVHD) is the most common complication of hematopoietic stem cell transplant (HCT). However, our understanding of the molecular pathways that cause this disease remains incomplete, leading to inadequate treatment strategies. To address this, we measured the gene expression profile of non-human primate (NHP) T cells during acute GVHD. Utilizing microarray technology, we measured the expression profiles of CD3+ T cells from five cohorts: allogeneic transplant recipients receiving 1) no immunoprophylaxis (No Rx); 2) sirolimus monotherapy (Siro); 3) tacrolimus-methotrexate (Tac-Mtx); as well as 4) autologous transplant recipients (Auto) and 5) healthy controls (HC). This comparison allowed us to identify transcriptomic signatures specific for allo-reactive T cells and determine the impact of both mTOR and calcineurin inhibition on GVHD-mediated pathway dysregulation. We found that the transcriptional profile of unprophylaxed GVHD was characterized by significant perturbation of pathways regulating T cell proliferation, effector function and cytokine synthesis. Within these pathways we discovered potentially druggable targets not previously implicated in GVHD, prominently including aurora kinase A (AURKA). Utilizing a murine GVHD model, we demonstrated that pharmacologic inhibition of AURKA could improve survival. Moreover, we found enrichment of AURKA transcripts both in allo-proliferating T cells and in sorted T cells from patients with clinical GVHD. These data provide a comprehensive elucidation of the T cell transcriptome in primate acute GVHD. This transcriptome enables a systems-based approach to the identification of targets for disease control, many of which are immediately amenable for clinical evaluation. The first such target identified, AURKA should now be considered a lead target for prevention of GVHD, which, given the many available AURKA inhibitors in clinical development, could be quickly deployed for the prevention of GVHD.