Glycoconjugates in the kidney play an important role in the maintenance of glomerular filtration barrier. Thickening of the glomerular basement membrane (GBM) is well characterized in diabetic nephropathy. Changes in GBM mainly include reduction and undersulfation of heparan sulfate, and laminin with accumulation of type IV collagen leading to kidney dysfunction and there is a need to identify therapies that arrest disease progression to end-stage renal failure. In the present investigation, effect of bitter gourd on streptozotocin-induced diabetic rats with particular emphasis on kidney heparan sulfate (HS) was studied. Earlier, our study showed partial reversal of all the diabetes-induced effects by bitter gourd. Increase in the components of glycoconjugates during diabetes was significantly decreased by bitter gourd feeding. Diabetes associated elevation in the activities of enzymes involved in the synthesis and degradation of glycosaminoglycans (GAGs) were significantly lowered by bitter gourd supplementation. GAGs composition revealed decrease in amino sugar, and uronic acid contents during diabetes and bitter gourd feeding was effective in countering this reduction. Decrease in sulfate content in the GAGs during diabetes was ameliorated by bitter gourd feeding. HS decreased by 43% in diabetic rats while bitter gourd feeding to diabetic rats showed 28% reduction. These results clearly indicate beneficial role of bitter gourd in controlling glycoconjugate and heparan sulfate related kidney complications during diabetes thus prolonging late complications of diabetes.