An NMR-metabonomic study of malformed fetuses was carried out through human amniotic fluid (HAF) analysis. Over 70 compounds were detected in control HAF by NMR. Possible confounding variables (fetus gender and gestational and maternal ages) were shown not to induce detectable compositional trends in the control group considered. Malformed fetuses showed variations in glucose, some amino acids and organic acids and proteins. In tandem with enzymatic assays, these NMR results suggest that changes in gycolysis and gluconeogenesis as well as kidney underdevelopment occur in the malformed fetuses studied here.