We localized endogenous anti-thrombin III (ATIII) by light and electron microscopic immunocytochemical staining in cryostat and ultra-thin frozen sections of 10 different rat tissues, using rabbit alpha-human ATIII antibody that was shown to crossreact strongly with rat ATIII. EM immunocytochemical methods revealed discrete deposits of endogenous ATIII (absent after heparinase treatment), and thus by inference anticoagulantly active heparan sulfate proteoglycans (HSPGs) at a resolution of 10-20 nm, or an order of magnitude better than autoradiography or LM. ATIII was found in variable amounts almost entirely in the subendothelial space of blood vessels in various rat tissues. In kidney, ATIII was found immediately beneath the endothelium, in concentrated clusters associated with the vascular basement membrane. Equally important is the observed variation in expression of ATIII in the various tissues studied (i.e., kidney > liver, aorta, lung, spleen, adrenal > intestine, muscle, brain). On the basis of these observations, we confirm a model in which vascular abluminal and, perhaps to a much smaller extent, luminal anticoagulantly active HSPGs regulate coagulation mechanism activity, either by serving as a reserve of anticoagulant or by modulating the ambient function of the coagulation cascade.