Proton-induced X-ray emission (PIXE) combined in Kossel geometry was developed as a non-destructive structural characterization method of nanometer thin films deposited on Si. The method is applied to study Pt/Fe/Pt and Ta/Cr/Pt thin films designed as X-ray planar waveguides. With the help of an energy dispersive X-ray camera, the intensities of characteristic X-ray emissions versus the detection angle (grazing exit), called Kossel curves, were measured. It is found that an interfacial compound is formed in Pt/Fe/Pt waveguide, whereas oxidation and mixing occur in the Ta/Cr/Pt system. It was not possible to obtain the description of the successive layers when considering only grazing incidence x-ray reflectivity. When PIXE-Kossel experiments are also considered, supplementary constraints have to be fulfilled when fitting the values of the stack parameters (number, composition, thickness, roughness and density of the layers) which restrict the possible descriptions of waveguides. Thus PIXE-Kossel is suitable to characterize stacks of nanometer thin films designed to be applied as an x-ray waveguide.