SrTiO3 is a widely used substrate for the epitaxial growth of complex systems. Nevertheless, in order to get good quality interface and avoid the formation of defects in the adsorbed layer it is essential to prepare the surface of the substrate prior to the deposition. Thermal and chemical treatments are mostly used to eliminate superficial contamination and improve the surface quality. However, there is a lack of information regarding the impact of these treatments on the formation of structural defects at the SrTiO3 surface. In this work we present a detailed characterization of the SrTiO3 surface for the different cleaning methods paying special attention to the formation of oxygen vacancies, large surface mosaicity and roughness. We prove that thermal treatment induces large surface roughness and that chemical etching produces important structural defects at the surface. Our results show that mechanical polishing provided the best compromise in terms of large surface domains, low roughness, absence of oxygen vacancies and absence of atomic structure modification, although with the presence of low level of contaminants at the SrTiO3 surface. (C) 2017 Elsevier B.V. All rights reserved.