Objectives: Down syndrome is the most common human chromosomal aberration. It is commonly known that it is a genetic-based disease, but still, pathomechanisms which lead to observed disorders have not been explained. The objective of this study was to determine the metabolic fingerprinting of the amniotic fluid women carrying foetuses with Down syndrome (DS). Material and methods: The study and control groups consisted of women who underwent routine amniocentesis between the 15 th and 18 th week of gestation. After analysis of the karyotyping results, 13 women with foetal DS were chosen. For the control group, 13 healthy patients with uncomplicated pregnancies who delivered healthy newborns at term was selected. Amniotic fluid was analyzed using liquid chromatography combined with high resolution mass spectrometry. Results: In the amniotic fluid of women with foetal DS compared to patients with healthy foetuses, we reported significant differences in the level of four metabolites: methylhistidine, hexanoylcarnitine, diacetylspermine and p-cresol sulfate which may be connected with improper development of nervous system and muscles. We detected bacterial metabolite, which support the latest thesis about non-sterile intrauterine environment. Conclusions: Based on our findings, we hypothesise that differences in the level of four metabolites in the amniotic fluid may play role in the pathogenesis of DS. Defining their potential as biochemical pathogenic factors of DS requires further investigation of the biological pathways involving in the foetal development.