A method of sample surface topography reconstruction is described based on the asymmetry in the X-ray yields acquired by a pair of X-ray detectors positioned at opposite sides of the probing beam. The yield asymmetries in the two simultaneously acquired elemental maps are caused by differences in the X-ray absorption along the X-ray exit route in the sample with a topographically structured surface. The approach presented introduces an asymmetry factor of the X-ray intensity in each of the image pixels to obtain an image asymmetry matrix. The dependence of the asymmetry factor on the local target inclination in the detector plane is calculated for a flat sample surface model. The image asymmetry matrix is then converted into the local inclination angle matrix. As the last step, the surface topography is then reconstructed from the local inclination angle. The method is based on X-ray absorption phenomena and could be applied equivalently in X-ray elemental mapping methods using excitation beams with a well-defined direction in the sample. This includes micro-X-Ray Fluorescence analysis (micro-XRF) and micro-Proton Induced X-ray Emission (micro-PIXE). We demonstrated the method by topographic analysis of engraved metallic samples with stereo-PIXE and compared it with the results of stylus profilometry. The smallest value of the X-ray production depth and the characteristic X-ray attenuation length determines the lateral resolution of the proposed topography reconstruction method.