Changes in cell and tissue organization and in peroxidase activity have been analyzed to find early markers to predict graft incompatibility occurrence in peach/plum combinations (Prunus persica/Prunus spp.) at 5 months after grafting in the dormancy period. Different compatible and incompatible peach/plum grafts were grown for 5 months in a nursery. The cellular study of the graft interface revealed structural changes associated with graft incompatibility symptoms. The main structural features were cambium cell disorganization, less differentiation of vascular tissues, degeneration of phloem and xylem cells, and accumulation of phenols at the graft interface after 5 months of graft development. The peroxidase study was performed during dormancy and the vegetative growth period, and revealed a significant increase in peroxidase activity in the incompatible unions, with significant differences between compatible and incompatible grafts. Analysis of gel profiles of nonbudded rootstocks and scions revealed an anodal isoperoxidase band [relative front (Rf) = 0.48] present in scions and compatible rootstocks, and another isoperoxidase band (Rf = 0.53) only present in the incompatible rootstocks. Our results show that the analysis of cell organization to detect early structural events and the evaluation of peroxidase activity at graft unions constituted feasible and convenient methods for early diagnosis of graft incompatibility. Also, it was suggested that the presence of band Rf = 0.48 in plum rootstocks and peach cultivars could be used as a marker to predict graft compatibility for peach scions and plum rootstocks.