We evaluated the effect of streptozotocin-induced diabetes on the structures of dermatan sulfate (DS) and heparan sulfate (HS) prepared from rat submandibular gland glycosaminoglycans (GAGs). GAGs were isolated and purified from the submandibular glands of diabetic and age-matched control rats by standard procedures. DS and HS were prepared from GAG by chondroitinase AC and ABC digestions. The unsaturated disaccharides produced from DS and HS by enzymatic digestion were separated and identified by HPLC. The unsaturated disaccharides from DS in normal rats had ΔDi-4 S as its main component and ΔDi-6 S and ΔDi-0 S as subcomponents. The proportion of ΔDi-4 S increased in diabetes along with a decrease in ΔDi-0 S. The unsaturated disaccharides from HS in normal rats were identified as ΔDiHS-0 S, which was the main component, and ΔDiHS-6 S and ΔDiHS-NS, which were subcomponents. However, the ratio of the peak height of ΔDiHS-0 S to that of ΔDiHS-6 S increased in diabetes. This suggests that diabetes causes a reduction in the non-sulfated portion of the DS chain, and an increase in the non-sulfated portion of the HS chain.