In case of very small nanocrystals, the surface is the dominant defect, generating a microstructure as deviation from the ideal crystal structure by breaking the translational symmetry of the lattice. This heterogeneous disorder may be observed as a different local structure in the core and shell of the nanocrystals and is highly relevant in all properties and applications for which defects are detrimental or beneficial, for example, charge-carrier traps in (opto-)electronics or active surface sites in heterogeneous catalysis. Very small SnO 2 nanocrystals generated by chemical vapor synthesis with coherent diffracting domain sizes between 2 and 13 nm are investigated as a model system since they form phase-pure stannic oxide isostructural to rutile. Local structure, crystal structure, and microstructure are studied using X-ray absorption spectroscopy, wide-angle X-ray scattering, X-ray diffraction, and transmission electron microscopy analyzed using reverse Monte Carlo simulations, Rietveld refinement, and image analysis. Size, surface, and interface effects as well as structural defects are discussed. The fraction of atoms at surfaces is substantial for very small nanoparticles. However, only very subtle structural changes are observed here for very small SnO 2 nanocrystals as revealed by detailed quantitative structural analysis. This may be because the particles are highly crystalline even for the ultrasmall 2 nm particles which are close to the molecular cluster regime.