The intercellular spaces between neurons and glia contain an amorphous, negatively charged extracellular matrix (ECM) with the potential to shape and regulate the distribution of many diffusing ions, proteins and drugs. However, little evidence exists for direct regulation of extracellular diffusion by the ECM in living tissue. Here, we demonstrate macromolecule sequestration by an ECM component in vivo, using quantitative diffusion measurements from integrative optical imaging. Diffusion measurements in free solution, supported by confocal imaging and binding assays with cultured cells, were used to characterize the properties of a fluorescently labeled protein, lactoferrin (Lf), and its association with heparin and heparan sulfate in vitro. In vivo diffusion measurements were then performed through an open cranial window over rat somatosensory cortex to measure effective diffusion coefficients (D*) under different conditions, revealing that D* for Lf was reduced Ϸ60% by binding to heparan sulfate proteoglycans, a prominent component of the ECM and cell surfaces in brain. Finally, we describe a method for quantifying heparan sulfate binding site density from data for Lf and the structurally similar protein transferrin, allowing us to predict a low micromolar concentration of these binding sites in neocortex, the first estimate in living tissue. Our results have significance for many tissues, because heparan sulfate is synthesized by almost every type of cell in the body. Quantifying ECM effects on diffusion will also aid in the modeling and design of drug delivery strategies for growth factors and viral vectors, some of which are likely to interact with heparan sulfate.drug delivery ͉ extracellular matrix ͉ integrative optical imaging ͉ somatosensory cortex ͉ transferrin T he spread of diffusible signals in brain extracellular space (ECS) is influenced by the local environment, with clearance mechanisms and the ECS volume fraction, tortuosity, and width among the best appreciated factors (1-3). The role that brain extracellular matrix (ECM) components play in modulating diffusion is less understood. Normal brain ECM is composed mostly of hyaluronic acid, a nonsulfated glycosaminoglycan, and proteoglycans carrying either chondroitin sulfate (CSPG) or heparan sulfate (HSPG) glycosaminoglycan side chains, along with the more recently identified reelin and tenascin glycoproteins (4, 5). Although aging (6-8), pathological insults (9, 10), or genetic modifications (11) resulting in altered brain ECM content are often associated with changes in ECS volume fraction, the ability of ECM components to specifically bind and slow the migration of diffusing substances in the ECS remains an open question. A direct ECM effect on extracellular diffusion (e.g., sequestration or slowing of a diffusing substance) has been postulated for proteins capable of binding HSPG (12, 13), but little evidence exists for this phenomenon in vivo.HSPGs are thought to play essential roles in the physiology of all organ systems (14). They compris...