Abstract By means of atomic force microscopy, we have investigated the surfaces of SrTiO 3(001) substrates (used for the growth of high- T c superconducting films) after different heat treatments. These treatments were (i) annealing in O 3, (ii) annealing in O 2, (iii) annealing in O 3 followed by deposition of SrTiO 3, and (iv) annealing in UHV. Our results suggest that, independently of the type of annealing, the surfaces of the polished SrTiO 3 substrates rearrange, either by diffusion or desorption of atoms, until reaching the energetically most favourable surface structure. For vicinal (001) substrates, this equilibrium structure corresponds to atomically flat terraces separated by smooth steps of one unit-cell in height, with the orientation and width of the terraces being determined by the miscut of the substrate. However, the kinetics involved in the reconstruction of the SrTiO 3 surface were observed to be strongly dependent on the annealing conditions. In particular, the use of O 3 instead of O 2 or UHV was found to accelerate the reconstruction of the SrTiO 3 surface. Finally, this study provides an accurate characterisation of the defects present on SrTiO 3 substrates.