The effects of several cross-linking reagents on mouse brain synaptosomal plasma membrane and synaptic junction fractions were examined and compared. The rate of cross-linking by dimethyl suberimidate of many synaptosomal plasma membrane polypeptides was inversely correlated with their size, and these species were found together in cross-linked complexes fractionated on Sepharose 2B; several low molecular weight species, however, believed to include tubulin and actin, were cross-linked relatively slowly and were preferentially found in fractionated complexes of highest molecular weight. In contrast to those of synaptosomal plasma membrane, most of the polypeptides of synaptic junctions were cross-linked with the shorter molecule dimethyl adipimidate, and the rate of this process did not bear any marked relationship with molecular weight. Many of these species were found to be cross-linked in situ with disulfide bonds, as previously reported by others; the molecular weight of these in situ complexes was greater than 40 X 106. Most of the in situ cross-links were cleaved by treating intact synaptic junctions with B-mercaptoethanol, but species of such reduced preparations were still cross-linked with adipimidate or o-phenanthroline-Cu2+. These results suggest that many polypeptides in synaptosomal plasma membrane are freely mobile and probably randomly distributed in the lipid bilayer, while several structural proteins may exist in ordered arrays. All of the species in the synaptic junction, in contrast, appear to be immobilized; some of these polypeptides are linked by disulfide bonds, while others are joined by noncovalent bonds and may form bridges between disulfide-linked species. The synaptic junction complexes may form one continuous network in this specialized membrane.