CdTe thin film solar cells were deposited by close-space sublimation (CSS) at substrate temperatures of 310 °C (low temperature) and 500 °C (high temperature). The microstructure of the layers was investigated on ionpolished cross sections of the solar cells by field emission scanning electron microscopy (FE-SEM). The low temperature CdTe layer is characterized by a columnar microstructure with lateral grain sizes between 0.2 and 0.7 μm in direction of layer growth and some porosity at grain boundaries. In contrast, the high temperature CdTe layer exhibits a dense, block-like microstructure with large grains between 1 and 2 μm. After CdCl2 activation process the low temperature layer is recrystallized into a globulitic microstructure with a mean grain size of 1.2 μm, whereas no significant change in microstructure was observed for the high temperature layer. It can be shown by glow discharge optical emission spectrometry (GD-OES) that the low temperature CdTe layer contains a drastically higher chlorine content than the high temperature layer. This result can be explained by higher amount of grain boundary diffusion and simultaneous recrystallization of low temperature CdTe layer during activation treatment. The different grain structures have also a strong influence on the registered electron beam induced current (EBIC) signal distribution. The low temperature CdTe layer exhibits a relative homogenous EBIC signal after activation treatment, whereas for the high temperature CdTe layer the grain boundary near regions deliver a drastically higher EBIC signal.