Silicon-germanium thin films have been analyzed by EDS microanalysis in a field emission gun scanning transmission electron microscope (FEG-STEM) equipped with a high angular dark-field detector (STEM/HAADF). Several spectra have been acquired in the same homogeneous area of the cross-sectioned sample by drift-corrected linescan acquisitions. The Ge concentrations and the local film thickness have been obtained by using a previously described Monte Carlo based “two tilt angles” method. Although the concentrations are in excellent agreement with the known values, the resulting confidence intervals are not as good as expected from the precision in beam positioning and tilt angle position and readout offered by our state-of-the-art microscope. The Gaussian shape of the SiKα and GeKα X-ray intensities allows one to use the parametric bootstrap method of statistics, whereby it becomes possible to perform the same quantitative analysis in sample regions of different compositions and thicknesses, but by doing only one measurement at the two angles.