Changes in glomerular anionic sites were examined morphometrically in nephrotic rats receiving daily subcutaneous injections of puromycin aminonucleoside (PAN). The high-iron diamine-thiocarbohydrazide-silver proteinate method showed that anionic sites composed of heparan sulfate proteoglycans formed a continuous band within the lamina rara externa of the glomerular basement membrane (GBM) in control rats. Only one day after the first injection of PAN, anionic site loss was already detectable, preceding the morphological changes in the epithelial cells. The number and size of the anionic sites decreased greatly between days 7 and 10, when urinary protein excretion began to appear. The number of anionic sites in the paramesangial regions (epithelial side of the mesangium) was slightly more reduced than that in the capillary walls. These results suggested that PAN directly injured the glomerular anionic sites and increased the permeability of the glomerulus to macromolecules. However, there was no complete correlation between the number of lost anionic sites and the level of urinary protein excretion. Thus protein excretion into the urinary space may be related not only to the loss of subepithelial anionic sites but also to dysfunction of the protein absorption mechanism in epithelial cells due to excessive permeation of macromolecules through the GBM.