Grafting is a technique applied to a considerable number of crops, with tomato standing out. However, this technique is limited by the obtaining of unfunctional grafts, which decrease the success rate and therefore the benefits achieved. The aim of this work was to analyze the failure in intraspecific grafting of tomato plants, focusing on tissue development, cell wall defense reactions, and the distribution of starch and soluble sugars at the graft junction. The success rate in autografts was higher than that of homografts and heterografts. Unfunctional homografts and heterografts showed similar responses: absence of vascular reconnections and lack of adhesion between scion and rootstock, even though callus cell clusters and differentiation of new vasculature were produced. The scions of unfunctional grafts accumulated more starch and soluble sugars than the rootstocks, showing a strong asymmetry in the response. In addition, three types of deposits were observed in the cell walls of unfunctional grafts: lignin, suberin, and callose, with the combined accumulation of more than one of them being frequent, particularly lignin and suberin. These deposits apparently prevent adhesion and seem to be a major cause of graft failure.