To characterize the structural events associated with incompatibility of graft development, we conducted a histological study of compatible and incompatible pear/pear and pear/quince grafts that had been grown for five months in a greenhouse. Multivariate analysis of histological data describing the structure of the graft union allowed us to discriminate between compatible and incompatible combinations before either macroscopic examination or qualitative microscopic examination differences between graft combinations became evident. The histological variables responsible for the discrimination between incompatible and compatible unions were related to three typical symptoms of graft incompatibility: bark discontinuity, which was the main feature; cambial dysfunction; and accumulation of starch in the scion. Little cell necrosis was observed at the interface of incompatible grafts at the 5-month stage of graft development. Multivariate analysis of histological data provides a new tool for studying early structural events resulting from the graft incompatibility response and for diagnosing early graft incompatibility.