This paper proposes a methodology designed to tackle the most common problems of MPI parallel programs. By developing a methodology that applies simple steps in a systematic way, we expect to obtain the basis for a successful autotuning approach of MPI applications based on measurements taken from their own execution. As part of the Au-toTune project, our work is ultimately aimed at extending Periscope to apply automatic tuning to parallel applications and thus provide a straightforward way of tuning MPI parallel codes. Experimental tests demonstrate that this methodology could lead to significant performance improvements.