Nanocrystalline anatase powders synthesised by various chemical processes as super/subcritical fluid extraction, sol-gel technique and hydrolysis of titanium alkoxides in hydrogen peroxide were studied by X-ray diffraction (XRD) whole profile modelling method (WPPM) in order to reveal correlations between structural and micro-structural parameters as well as sample treatment conditions. Anisotropy of the diffraction line broadening due to truncated bipyramidal shape of anatase crystals was discussed. The hkl-anisotropy can be very strong but also almost negligible in dependence on relative ratio of the crystallite dimensions. The latter was the case for the studied samples. The size of synthesised anatase nanoparticles was within the range 3–25 nm. The theoretical total surface area of crystallites calculated from XRD was in a good correlation with the surface area measured by the nitrogen physisorption up to the temperature 400–450 °C, when the particles started to agglomerate. At atomic scale a unit cell volume contraction with decreasing crystallite size and a significant deficiency in the Ti-site occupancy was observed. Both effects were attributed to the presence of Ti-vacancies and a linear coefficient between the relative cell volume contraction and the fraction of Ti-vacancies was estimated to (–0.017 ± 0.003).