3D die stacking is a promising technique to allow miniaturization and performance enhancement of electronic systems. Key technologies for realizing 3D interconnect schemes are the realization of vertical connections, either through the Si die or through the multilayer interconnections. The complexity of these structures combined with reduced thermal spreading in the thinned dies complicate the thermal analysis of a stacked die structure. In this paper a methodology is presented to perform a detailed thermal analysis of stacked die packages including the complete back end of line structure (BEOL), interconnection between the dies and the complete electrical design layout of all the stacked dies. The calculations are performed by 3D numerical techniques and the approach allows importing the full electrical design of all the dies in the stack. The methodology is demonstrated on a 2 stacked die structure in a BGA package. For this case the influence of through-Si vias (TSVs) on the temperature distribution is studied. The modeling results are experimentally validated with a dedicated test vehicle. A thermal test chip with integrated heaters and diodes as thermals sensors is used to successfully validate the detailed temperature profile of the hot spots in the top die of the die stack.