Urinary heparan sulfates (HS) from two siblings with mucopolysaccharidosis (MPS) III-B were fractionated by chromatography with Dowex 1 and Sephadex G-50. Their Mr ranged from 1600 to 8000, and 95% of them were included in the region less than 5000. Fractions with lower Mr contained larger amounts of 0-and N-sulfates. The chemical analysis and deaminative cleavage of HS suggested that an intact HS molecule was composed of some blocks rich in G1cNAc and G1cUA and other blocks rich in G1cNS, IdUA and 0-sulfate. G1cNAc-UA-G1cNS-UAG1cNAc-UA-G1cNAc was found to be a major oligosaccharide of HS with Mr less than 1800. Trisaccharides, G1cNAc-G1cUA-aMan and G1cNAc-IdUA-aMan, were released from the nonreducing end of HS-oligosaccharides by deaminative cleavage. They carried 0-3 moles of ester sulfate. G1cNAc-IdUA-aMan was more sulfated than the other. The release of significant amounts of nonsulfated trisaccharide conform to the enzyme defect in this disease. Urinary HS obtained from another patient with MPS III were examined by the same way. Although the patient was not examined enzymatically, the structure of urinary GAG suggested a defect of a-N-acetylglucosaminidase in the patient.Sanfilippo syndrome ; mucopolysaccharidosis III-B ; urinary glycosaminoglycan ; heparan sulfate ; oligosaccharide structure Patients with MPS excrete in their urine an excessive amount of GAG with low Mr, which is a favorable material to study the structure or catabolic process of GAG. In our previous studies, it was shown that the urinary DS from patients with Hurler-Scheie syndrome (MPS I-H/S) had an IdUA residue at the nonreducing end, and only 50% of excess sulfate were bound to inner IdUA residues