Central nervous system diseases are neurological disorders that affect the structure or function of the brain and spinal cord that make up the central nervous system. In this study, it was aimed to examine the impaired/altered metabolomic profiles of pregnant women carrying fetuses with nervous system abnormalities (NSA). The study group consisted of 30 normal pregnancies with normal fetuses (control group) and 8 pregnancies with fetuses having NSA (study group), as determined by prenatal screening and diagnosis as part of an antenatal care program. Metabolomic analyses were carried out using gas chromatography-mass spectrometry (GC-MS). GC-MS-based metabolomics analysis was able to identify 95 metabolites and 27 of them were statistically significant between the two groups (p<0.05). Moreover, the pathway analysis, performed with significantly altered metabolites, showed alteration in the alanine, aspartate, and glutamate metabolism, citrate cycle, aminoacyl t-RNA biosynthesis, and glutathione metabolism. Alanine, aspartate and glutamate metabolism, citrate cycle, aminoacyl t-RNA biosynthesis, and glutathione metabolism seem to be critical in the prenatal screening of NSAs. However, abnormality-specific studies are necessary for further recommendations.