We have used small-angle x-ray scattering (SAXS) in conjunction with X-ray diffraction (XRD) to study the nanostructure of hydrogenated nanocrystalline silicon (nc-Si:H). The crystallite size in the growth direction, as deduced from XRD data, is 24 nm with a preferred  orientation in the growth direction of the film. Fitting the SAXS intensity shows that the scattering derives from electron density fluctuations of both voids in the amorphous phase and H-rich clusters in the film, probably at the crystallite interfaces. The SAXS results indicate ellipsoidal shaped crystallites about 6 nm in size perpendicular to the growth direction. We annealed the samples, stepwise, and then measured the SAXS and ESR. At temperatures below 350◦C, we observe an overall increase in the size of the scattering centers on annealing but only a small change in the spin density, which suggests that bond reconstruction on the crystallite surfaces takes place with high efficacy.