We address the accuracy of Energy Dispersive X-ray Spectroscopy (EDS) composition analysis of YBa2Cu3O7-x (YBCO) thin films. YBCO films deposited on yttrium stabilized zirconia (YSZ) and strontium titanate (STO) substrates were analyzed by EDS and Rutherford Backscattering Spectrometry (RBS) to determine their compositions. The YSZ substrates used in this work contained a common element, yttrium; therefore, EDS intensities of yttrium signals resulting from the film alone were calculated using EDS results of blank YSZ substrates. The EDS compositions of all the elements were obtained using the proportionality factor, k calculated from RBS data from a standard film deposited on silicon and the intensity ratios of the respective standard obtained from EDS. The film thickness was found to be an important factor to consider when choosing the optimum accelerating voltage for the EDS analysis. For films having comparable thickness to that of the standard (similar to 0.8 mu m), we found 25 kV was the optimum accelerating voltage for the EDS analysis that obtained compositions in good agreement with the RBS data. For films having half the thickness of the standard film, EDS composition analyses were unreliable quantitatively and were best qualitatively at 15 kV.