We investigated the differential distribution of basement membrane type IV collagen a chains in the mouse brain by immunohistochemistry using a chain-specific monoclonal antibodies. Subendothelial basement membranes were found to contain alpha1 and alpha2 chains. Basement membranes surrounding smooth muscle cells on blood vascular walls were immunoreactive for alpha1 and alpha2 chains but not for alpha5 and alpha6 chains. Interestingly, the pia mater contained a thin basement membrane which was positive for alpha1, alpha2, alpha5, and alpha6 chains, suggesting that glia limitans superficialis coheres basement membranes containing [alpha1(IV)]2alpha2(IV) and [alpha5(IV)]2alpha6(IV) molecules. In contrast, capillaries always possessed thin basement membranes of [alpha1(IV)]2alpha2(IV) molecules. Cerebrospinal fluid is produced through filtration of blood at the choroid plexus, where two distinct basement membranes were detected by anti-al and anti-alpha2 antibodies. The subendothelial basement membrane appeared to consist of [alpha1(IV)]2alpha2(IV) molecules, whereas the subependymal basement membrane in the choroid plexus was strongly positive for alpha3, alpha4, and alpha5 chains, indicating that the filtering unit was composed of alpha3(IV)alpha4(IV)alpha5(IV) molecules. That the specific localizations of these molecules are shared by renal glomeruli and the choroid plexus leads us to hypothesize that the supramolecular network containing alpha3(IV) alpha4(IV)alpha5(IV) molecules may function as a permeability selective barrier.