Aim: In this study the authors aimed to evaluate whether there are any causal relationship between heavy metals-trace elements and fetal malformations of central nervous system (CNS). Materials and Methods: The study group consisted of pregnancies with fetal congenital nervous system anomaly (anencephaly, acrania, neural tube defects, etc.) in 16-22 weeks (n=36). Pregnancies with the same weeks of pregnancy who underwent amniocentesis due to high risk in triple test with the result of normal karyotype constituted the control group (n=30). In the both groups the authors analyzed the heavy metals and trace elements in amniotic fluid. Metals and elements were measured by using atomic absorption spectrophotometer technique with a UNICAM-929 spectrophotometer. Results: When compared, the groups were similar in terms of age, parity, BMI, and gestational week (p > 0.05). In fetal congenital anomaly group the authors detected low levels of copper (Cu) and zinc (Zn) rather than control groups (p < 0.05). In fetal congenital anomaly group they detected high levels of lead (Pb) and cadmium (Cd) rather than control groups (p < 0.05). Iron (Fe), manganese (Mn), cobalt (Co), nickel (Ni), and Cd levels were similar and there was no significantly difference between the groups (p > 0.05). Conclusion: This study can contribute benefits to the literature in terms of clarifying the pathogenesis of fetal congenital nervous system anomalies.