Our objective was to measure amniotic fluid amino acid concentrations in pregnant women diagnosed as having fetuses with non immune hydrops fetalis in the second trimester of pregnancy. Twenty-three pregnant women who had fetuses with non immune hydrops fetalis detected by ultrasonography (non immune hydrops fetalis group) in the second trimester and 19 women who had healthy fetuses (control group) were enrolled in the study. Amniotic fluid was obtained by amniocentesis. The chromosomal analysis of the study and control groups was normal. Levels of free amino acids were measured in amniotic fluid samples using EZ: fast kits (EZ: fast GC/FID free (physiological) amino acid kit) by gas chromatography (Focus GC AI 3000 Thermo Finnigan analyzer). The mean levels of alanine, cysteine, glycine and valine amino acids were found to be significantly higher in fetuses with non immune hydrops fetalis than in the control group (p < 0.05). The detection of significantly higher amino acid concentrations in the amniotic fluid of fetuses with a non immune hydrops fetalis in healthy fetuses suggests loss of amino acids from the fetus through capillary permeability or/and the lymphatic system through the amniotic fluid may contribute to the etiology of non-immune hydrops fetalis.