Using a cellular digestion technique combined with scanning electron microscopy, we examined the three-dimensional ultrastructural changes of the glomerular basement membrane (GBM) in various types of human glomerulonephritis (GN). Gaps of the GBM, which were not found by routine transmission electron microscopy, were observed in a patient with IgA nephropathy manifesting microscopic hematuria. The dense material of the GBM in dense deposit disease (DDD) was not affected by this cellular digestion technique, while the deposits in other immune complex diseases were almost removed. Thus the dense material in DDD differs in composition from the immune complex deposits in other GN. In membranous GN and lupus nephritis, the morphological changes of the urinary surface of the GBM varied from pinhole to craters and reticula, according to the severity of the disease stage. This technique is useful for examining ultrastructural changes of the GBM in various human GN.