The re-crystallization of thin film cadmium telluride (CdTe) using the cadmium chloride (CdCl2)annealing procedure is a vital process for obtaining high efficiency photovoltaic devices. Although the process is crucial, the precise micro-structural mechanisms at work are poorly understood. Recently it has been observed that untreated CdTe contains a high density of stacking faults and that these are removed in the CdCl2 assisted re-crystallization. In this paper, we report on experiments using magnetron sputtered CdTe to determine the effects of the re-crystallization process. In particular, we have focused on how the re-crystallization process initiates by using ultra-low concentrations of CdCl2 (0.06% and 0.03% of saturated CdCl2 in methanol). With these low concentrations a partial re-crystallization occurs, with the initiation occurring at the CdS/CdTe interface and not at the surface of the CdTe layer.