Compatibility of scion and stock combinations in Uapaca kirkiana fruit trees has not been evaluated despite noticeable growth irregularities. The objectives of this study were to determine graft compatibility of scion/stock combinations and possible causes of graft incompatibility. Scion, stock, and graft union diameters were measured. Stem sections comprising the graft unions were immersed in formalin acetic acid and then washed in sterile water. These were transversely dissected across the unions and examined under using light microscope. There were considerable growth disorders at the unions, which included significant overgrowth of stocks and unions and constricted unions. There were cracks in the bark across the union in many graft combinations. Anatomic and histological studies showed accumulation of phenol deposits and necrotic tissues, and there was no continuity of vascular tissues above the union. There were also differences in proliferation of callus tissues among grafted partners. Continuity in wood and bark tissues below the unions supported growth of partially compatible partners, whereas isolated parenchymatous tissues at the union supported growth of incompatible partners. There were many necrotic tissues and unfilled areas above the union. Accumulation of phenolic and necrotic cell deposits, poor or a high level of callusing at the union, and possibly specific incompatibility reactions were implicated as the causes of graft incompatibility in U. kirkiana trees.