Synaptic junction (SJ) were isolated by subcellular fractionation from different areas of the steer brain and from the brains of different species (steer, rat, chicken and human) for the purpose of comparing their protein and glycoprotein composition. The synaptic junction fractions from different brain regions and species were of comparable morphological purity. Analysis of the polypeptide composition of isolated synaptic junction fractions via SDS polyacrylamide gel electrophoresis showed that the major polypeptides were represented in all junctional fractions independent of their source. Tubulin, actin, the major 52,000 Mr postsynaptic density protein and a group of proteins with a molecular weight of 200-250,000 Mr were all similarly represented. Most other components were also similar but quantitative differences were found for a few polypeptides. Interspecies differences were more prevalent than those between different brain areas of the same species. The protein compositions of different brain areas were similar even when an area consisting of primarily one neuronal type was compared to areas containing a mixture of neuronal types. However, two-dimensional gel electrophoresis revealed distinct (but usually minor) polypeptides in enriched quantities in one or more brain areas. Tryptic peptide maps were carried out on the major postsynaptic density protein of different species. These maps showed a high degree of conservation in this protein's primary structure among all species studied. The glycoproteins of isolated synaptic junctions which bind the plant lectin concanavalin A (Con A) were also examined. To identify individual Con A binding components, SJ fractions were solubilized and constituent glycoproteins were separated by SDS gel electrophoresis. Gels were then incubated in 125I-Con A. The glycoproteins which bound Con A in gels were few in number and were not the major Coomassie blue staining bands. The great majority of the Con A binding glycoproteins were similar between species and among brain areas of the same species.