The structure of hydroxyapatite (HA) nanopowder has been determined by theta-scan precession electron diffraction (TS-PED) and Rietveld analysis. To evaluate the usefulness of the TS-PED technique, this result was compared with that of the Rietveld analysis using conventional electron diffraction (ED) and normal precession electron diffraction (PED). The intensity ratios of the (002) to (121) reflections (I002/I121) obtained by both PED data were in better agreement with the reference X-ray diffraction (XRD) data than that obtained by the conventional ED data. Although the lattice parameters of HA determined by the TS-PED data were slightly deviated from the reference XRD data, the a/c-axis ratio had the best agreement with the reference XRD data. The reliability factors (Rp, Rwp and χ2) of TS-PED refinement results were substantially improved, when compared with the values obtained by the conventional ED data. These results demonstrate that TS-PED technique could be a useful analytical method for structure determination of nanopowder.