Template Attacks and the Stochastic Model provide advanced methods for side channel cryptanalysis that make use of 'a-priori' know- ledge gained from a proling step. For a systematic comparison of Tem- plate Attacks and the Stochastic Model, we use two sets of measurement data that originate from two dieren t microcontrollers and setups. Our main contribution is to capture performance aspects against crucial pa- rameters such as the number of measurements available during proling and classication. Moreover, optimization techniques are evaluated for both methods under consideration. Especially for a low number of mea- surements and noisy samples, the use of a T-Test based algorithm for the choice of relevant instants can lead to signican t performance gains. As a main result, T-Test based Templates are the method of choice if a high number of samples is available for proling. However, in case of a low number of samples for proling, stochastic methods are an alter- native and can reach superior eciency both in terms of proling and classication.