The major proteins in isolated synaptic junctions (SJs) and postsynaptic densities (PSDs) have been compared to actin, tubulin, and the major neurofilament (NF) protein by two-dimensional gel electrophoresis and tryptic peptide map analysis. These studies show: (a) tubulin is present in SJ and PSD fractions and is identical to cytoplasmic tubulin, (b) actin in these fractions is very similar to the gamma- and beta-actin found predominantly in nonmuscle cells, and (c) the major PSD protein is distinct from all other known fibrous proteins.