The influence of the manufacturing technology on the structural properties of CdTe and CdS layers, components of the CdS/CdTe solar cells, has been investigated. CdTe based solar cells have been prepared using glass substrates coated with different transparent conductive oxides (TCOs:SnO2, In2O3:SnO2 (ITO), ZnO:Al, ZnO:Al/i-ZnO). The analysis of the technology combined with various investigation methods allowed to determine optimum deposition parameters for CdS and CdTe for each type of TCO used. X-ray diffraction (XRD) and grazing incidence XRD analysis have been carried out for TCO, CdS, and CdTe layers at different deposition stages before and after annealing in the presence of CdCl2 in air. The reflection spectra in the 100-600 cm(-1) spectral region have been thoroughly studied by using Fourier transform infrared spectroscopy. It was found that (i) the best quality possess CdS and CdTe thin films sequentially deposited on ZnO:Al substrates and that (ii) the pre-treatment defects can be effectively cured and most of the secondary phases can be removed by annealing, while the basic structure of the investigated thin films does not essentially change. (C) 2012 Published by Elsevier B.V.