The analysis of atomic ordering in a nanocrystalline phase with small particle size, below »5 nm, is intrinsically complicated because of the lack of long range order. Furthermore, the presence of additional crystalline phase(s) may exacerbate the problem as it is the case in cement pastes. Here we use synchrotron pair distribution function (PDF) chiefly to characterize the local atomic order of the nanocrystalline phases, gels, in cement pastes. We have used a multi r-range analysis approach, where the ~4-7 nm r-range allows determining the crystalline phase contents; the ~1-2.5 nm r-range is used to characterize the atomic ordering in the nanocrystalline component; and the ~0.2-1.0 nm r-range give insights about additional amorphous components. Specifically, we have prepared four alite pastes, with variable water contents, and the analyses showed that a defective tobermorite, Ca₁₁Si₉O₂₈(OH)₂^.8.5H₂O, gave the best fits. Furthermore, the PDF analyses suggest that the calcium silicate hydrate gel is composed of this tobermorite and amorphous calcium hydroxide. Finally, this approach has been used to study alternative cements. The hydration of monocalcium aluminate and ye'elimite pastes yield aluminum hydroxide gels. PDF analyses show that these gels are constituted by nanocrystalline gibbsite and the particle size can be as small as 2.5 nm.