The primary aim of this work was to investigate the ultrastructural morphology of the small intestinal mucosa in children affected by selective IgA deficiency (SIgAD). Absorptive tests and intestinal biopsies were performed in a group of nine children with SIgAD, none of them presenting with diarrhea. Biopsy specimens were processed for routine histology and scanning or transmission electron microscopy (SEM and TEM). By light microscopy, the jejunal mucosa appeared normal in all but one patient with patchy villous atrophy. By SEM, two further biopsies showed small areas of flat mucosa surrounded by villous ridges of nearly normal height. By TEM, four out of the nine mucosal specimens showed degenerative changes of the surface epithelium, including enlargement of the mitochondria, apical accumulation of primary and secondary lysosomes, and shortening and branching of the microvilli. These findings suggest that the small intestinal mucosa of children with SIgAD often shows pathological changes, some of which are recognizable only at the ultrastructural level. The study of biopsy specimens by SEM seems to be a useful diagnostic tool when patchy mucosal damage may occur, as in some of our patients with SIgAD.