A comparison of as-grown and processed CdTe/CdS solar cell structures deposited on sapphire substrate has been undertaken with those grown on glass. The device structures were depth-profiled using quantitative secondary ion mass spectrometry. It was shown that while Si concentration profiles are similar to those for structures grown on glass, Na was more than one order of magnitude lower when sapphire was used instead of glass, showing that Na diffused from the glass. It was also found that there was no measurable diffusion of Sn from the SnO2 layer into CdTe, and that the former played an important role in preventing the diffusion of In from In-containing transparent conducting oxide layer. Cl, O, Br, and F species were also investigated and while Cl and O were found to be independent of the nature of the substrate used, Br and F were shown to be affected by the processing.