In utero insults to growing fetus impact its health in adulthood. Glycosaminoglycans (GAGs) are involved in lipoprotein metabolism in the liver and vary both quantitively and qualitatively on feeding adult rats a diet rich in cholesterol. However, no reports are available to show the modulation of GAGs when the offspring are subjected to a high cholesterol diet in gestation and lactation stages. Hypercholesterolemia in pregnant rats was induced by feeding an AIN-93 diet supplemented with 0.5% cholesterol. The pups born to mothers fed with high cholesterol diet showed a significant increase in cholesterol and triglycerides accumulation in the liver. Quantitative changes in sulfated glycosaminoglycans (sGAGs), in particular of heparan sulfate, were observed across the developmental stages. Other players involved in lipoprotein metabolism, namely low-density lipoprotein receptor-related protein 1, apolipoprotein E, and low-density lipoprotein receptor expression levels, also showed differential changes across developmental stages. Interestingly, when pups from hypercholesterolemic mothers were fed a normal diet after weaning until adulthood, a considerable amount of fat accumulation in the liver was observed, implicating fetal exposure to early high cholesterol exposure on long term health.