This is the first study on structural and ultrastructural changes taking place in Actinidia deliciosa kiwifruits affected by "elephantiasis syndrome", by means of DRIFT, FT-Raman, NMR, and SEM techniques. The fruits arising from elephantiasis-affected plants assume a round and smaller shape, limiting their marketing. Despite etiological studies on this disease, so far no information is available on the structural and ultrastructural characteristics of the fruits. The SEM and spectroscopic data showed significant modifications regarding the polysaccharide fraction in kiwifruits from diseased plants. The pectins seem to be the polysaccharide fraction more involved in the structural variations of the fruits. These structural and ultrastructural variations are related to the elephantiasis syndrome, and they could be adopted as markers for early diagnosis of the disease.