We report effects of thermal annealing on the structures of Ge-Sb-Te (GST) nanoparticles synthesized by pulsed laser ablation deposition. The average diameter of the GST nanoparticles is an order of 10 nm. The as-prepared sample contains nanocrystals surrounded by an amorphous phase. Further crystallization occurs during annealing. The structures of the nanocrystals and amorphous phase were studied by electron diffraction and radial distribution function analyses. The results show that the nanoparticles annealed at 100 °C are crystalline, consisting of a mixture of face centered cubic (fcc) and hexagonal Ge2 Sb2 Te5 (dominant). In comparison, the nanoparticles annealed at 200 °C are mostly fcc. The surrounding amorphous phase has similar atomic arrangements to the previously reported amorphous GST thin films.