X-ray diffraction contrast tomography is used to investigate the crystallographic, topological and morphological characteristics of the evolving microstructure in thermally aged strontium titanate samples. The analysis of the 3D structure shows a clear signature of the grain boundary anisotropy, which can be correlated to surface energy anisotropy: the grain boundary orientation distribution function shows an excess of 〈100〉-oriented interfaces with respect to a random structure.