Glycosaminoglycans are polysaccharides involved in epithelial-mesenchymal interaction and cell differentiation and provide a meshwork which is essential to maintain a proper intercellular milieu. The development of embryonic organs can be accompanied by alterations in the glycosaminoglycan pattern. In pregnancies with malformed fetuses, there are alterations in total glycosaminoglycans and their components (chondroitin 4-6 sulphate, dermatan sulphate, and hyaluronic acid) in amniotic fluid. We examined total glycosaminoglycans and the percentage variations of the single classes in both amniotic fluid and culture medium of fibroblasts from heart, lung, and skin obtained from five normal human fetuses and one with holoprosencephaly. In the amniotic fluid total glycosaminoglycans and their sulphate classes were increased, whereas hyaluronic acid was decreased, compared with controls. The extracellular glycosaminoglycans showed hyaluronic acid reduction in skin, while chondroitin 4-6 sulphate plus dermatan sulphate and heparan sulphate were higher in skin and heart. Our data demonstrate that variations in the glycosaminoglycan pattern are associated with alterations of the cellular environment, which can prevent normal organogenesis.