It is well known that the crystalline structure of the III–V nanowires (NWs) is mainly controlled by the wetting contact angle of the catalyst droplet which can be tuned by the III and V flux. In this work we present a method to control the wurtzite (WZ) or zinc-blende (ZB) structure in self-catalyzed GaAs NWs grown by molecular beam epitaxy, using in situ reflection high energy electron diffraction (RHEED) diagram analysis. Since the diffraction patterns of the ZB and WZ structures differ according to the azimuth [10], it is possible to follow the evolution of the intensity of specific ZB and WZ diffraction spots during NW growth as a function of the growth parameters such as the Ga flux. By analyzing the evolution of the WZ and ZB spot intensities during NW growth with specific changes of the Ga flux, it is then possible to control the crystal structure of the NWs. ZB GaAs NWs with a controlled WZ segment have thus been realized. Using a semi-empirical model for the NW growth and our in situ RHEED measurements, the critical wetting angle of the Ga catalyst droplet for the structural transition is deduced.