We report a case of congenital renal proximal tubular dysfunction (CRPTD) accompanied by IgA nephropathy. The mesangial matrix was slightly increased with depositions of IgA and C3. Podocytes contained many clear vacuoles. Cuboidal cells, as well as squamous cells, lined the parietal epithelium of Bowman's capsule, although the functional or pathological significance of the cuboidal cells is unknown. The proximal tubular cells appeared to have a less-developed apical endocytic complex, basal infoldings and fewer lysosomes. These morphological changes may reflect proximal tubular dysfunction.