Heparan sulfate proteoglycans are consistently accumulated in tissues afflicted by amyloidosis and have been implicated in the mechanism of amyloid deposition. To study this relationship, heparan sulfate was isolated from liver and spleen of patients with AA amyloidosis and from normal organs and subjected to structural analysis. The polysaccharides were deaminated with nitrous acid, and the products were reduced with NaB3H4 to yield labeled oligosaccharides. Disaccharides obtained by selective deamination of intact or N-deacetylated polysaccharides were separated and quantified by anion-exchange high performance liquid chromatography and thus defined the composition of N-sulfated block regions or the entire heparan sulfate chains, respectively. The heparan sulfate samples derived from liver or spleen with AA-type amyloidosis were all similar in composition, regardless of tissue source, but differed from either control material. These findings suggest that secondary amyloidosis is associated with the deposition in the affected tissues of a heparan sulfate with a specifically modified structure.