A comparison between use of proton-induced x-ray emission (PIXE) and total reflection x-ray fluorescence (TXRF) techniques in relation to the elemental analysis of amniotic fluid (AF) was carried out by measuring the concentrations of Cl, K, Ca, Fe, Cu, Zn and Br. For 10 AF samples analyzed, the agreement between PIXE and a TXRF measurements was 100% for K, 60% for Cl and Ca, 80% for Fe and 50% for Cu. For Zn, although there was only a 20% agreement, the measured concentrations ranged between 0.1 and 1 μg/ml with a TXRF standard deviation as high as 0.070 μg/ml. For Br, a factor of 1.8±0.2 was obtained between TXRF and PIXE measurements, suggesting a systematic error between experiments. This work indicates that further investigation is required to determine the experimental conditions, e.g. sample preparation and irradiation, which lead to complete agreement between TXRF and PIXE when a complicated organic sample such as amniotic fluid is analyzed. Copyright © 1999 John Wiley & Sons, Ltd.