Small angle X-ray scattering (SAXS) is employed to characterize the inner structure and shape of aqueous nanocrystalline cellulose suspensions using the generalized indirect Fourier transformation (GIFT). The use of the GIFT approach provides a single fitting procedure for the determination of intra- and interparticle interactions due to a simultaneous treatment of the form factor P(q) and the structure factor S(q). Moreover, GIFT allows for the determination of particle charges and polydispersity indices. As test material, aqueous nanocrystalline cellulose suspensions (aNCS) prepared by the H2SO4 route have been investigated and characterized (SAXS, dynamic light scattering, zeta potential).