Material decomposition based on dual energy X-ray radiography which was primarily developed for tissue differentiation in medical imaging can be favorably used for composite material examination. The principle of this method is obtaining several absorption images of the sample with different energy spectra which allows for the identification of main material components. The need of measurement at several X-ray spectra can be achieved either by alternation of the tube voltage and/or by the use of additional filters. The single photon counting pixel detector Medipix allows direct energy discrimination of registered radiation enabling spectrum selection at the detector side without the need to first modify the X-ray source spectrum. Our approach provides moreover low noise images with broad dynamic range and thus high sensitivity and enhanced contrast. Utilization of a 3D voxel detector with two or more sensor layers allows obtaining all required images simultaneously in a single exposure. The results of the material decomposition obtained with the Medipix detector are presented and discussed in this contribution.