On immunofluorescence, types I and III MPGN usually show prominent granular capillary wall staining with C3, variable amounts of IgG and IgM, and sometimes C1q and C4. In contrast, in DDD the capillary wall typically stains with C3 in isolation.

The definitive distinction between MPGN subtypes can only be made with electron microscopy. In type I MPGN, immune deposits are seen in the subendothelium, whereas in type III they are also seen in the subepithelium. In DDD, pathognomonic electron-dense, intramembranous deposits are seen in the glomerular basement membrane. In many cases, these deposits are also present in the basement membranes of the tubules and arterioles. While the exact composition of the deposits has not been determined, they appear to contain glycoproteins similar to normal glomerular basement membrane, and they do not appear to contain antigenic material, immunoglobulins, or complement. In all subtypes, podocyte foot processes appear diffusely effaced.