Although the core protein of a heparan sulfate proteoglycan has been detected in brain microvessel basement membranes by immunoperoxidase staining, cytochemical evidence of a glycosaminoglycan component, in the form of discrete staining with ruthenium red, is not found. To resolve this discrepancy, we examined the glycosaminoglycan content of this basement membrane directly. Microvessels were isolated from pig cerebral cortex, and basement membranes freed from cellular elements. Following digestion with papain and Pronase, the glycosaminoglycans were precipitated with cetyl pyridinium chloride and ethanol. The resulting extract contained uronic acid, and after electrophoresis on Super Sepraphore revealed 2 bands: One co-migrated with heparan sulfate standard, the other with chondroitin sulfate A and C. The first was completely eliminated by nitrous acid and heparitinase, but not by hyaluronidase or chondroitinase ABC and was therefore confirmed as heparan sulfate; the other band was eliminated by chondroitinase ABC but not by the other three treatments. The findings suggest that basement membrane of brain microvessels, like other vascular basement membranes, contains heparan sulfate and chondroitin sulfate A and/or C. The failure of staining with ruthenium red is probably a result of unique structural features of this basement membrane, rather than an absence of glycosaminoglycan.