The immune response to transplanted allogeneic tissues is mediated by T cells that recognize donor histocompatibility Ags either via direct (donor MHC and peptides) or indirect (recipient MHC and donor-derived peptides) allorecognition pathways. The relative contribution of each of these pathways to allograft rejection remains largely unknown. To address this, we used an enzyme-linked immunospot assay to define the frequency and cytokine phenotype of T cells responding via direct and indirect pathways to alloantigens at various time points following placement of allogeneic B10.A skin grafts on BALB/c recipient mice. During acute graft rejection >90% of the anti-B10.A T cell repertoire was directed toward intact donor MHC molecules, while T cells recognizing indirectly presented, donor-derived peptides accounted for <10%. This indirect response was comprised of reactivity toward both MHC-derived and, to a lesser extent, minor Ag-derived determinants. The direct and indirect alloresponses were predominantly detected in recipient lymph nodes and were mediated by T cells displaying a mixed type 1/type 2 cytokine phenotype. Six weeks following rejection, however, the memory allospecific T cell response became predominant in the recipient spleen, with only minimal activity detectable in the draining lymph nodes. This work provides a new approach for analysis of the immunophysiology of allograft rejection and should be useful for monitoring immune responses to graft Ags in human transplant recipients.