Studies on the matrix effects of uranium and thorium on the determinations of each other in their mixed oxides using energy dispersive X‐ray fluorescence (EDXRF) spectrometry with tube and radioisotope excitations of U Lα and Th Lα are reported. An internal standard method for the determination of uranium and thorium in these mixed oxides is found suitable. Comparison of the analytical results of EDXRF determinations of uranium and thorium using tube and radioisotope excitation sources has been made. The analytical methodology involves preparation of mixed oxide calibration/sample mixtures of uranium and thorium oxides, mixing of internal standard yttrium in these mixtures, pelletizing the mixtures after thorough mixing and grinding using boric acid binder and measuring EDXRF spectra of the specimens thus prepared using Rh X‐ray tube as well as 109Cd radioisotope source. The samples were analyzed for uranium and thorium on the basis of the calibration plots obtained by plotting the intensity ratios of the analyte and internal standard characteristic X‐ray lines and their corresponding amount ratios. An average precision of 1.2% (1 s RSD) was observed for the determination of U and Th and the results deviated from the corresponding expected values by 3% on average. Due to the refractory nature of thorium oxide, comparatively more grinding time was required for thorium determinations. Copyright © 2011 John Wiley & Sons, Ltd.