The evolution of vacancy ordering structures in epitaxial YbSi2-x thin films on both (111) and (001)Si has been studied by transmission electron microscopy (TEM). Epitaxial YbSi2-x thin films were grown on Si by either room temperature deposition with subsequent thermal annealing or deposition at elevated temperature. Epitaxial YbSi2-x was found to form in samples annealed at 300 °C for 30 min and the appearance of additional diffraction spots is attributed to the formation of an ordered vacancy superstructure in the epitaxial YbSi2-x thin films. In other samples, the split or streaking of extra diffraction spots is attributed to the formation of out-of-step structures. The variation of out-of-step structures with the annealing temperature is correlated to a change in vacancy concentration that makes compressive stress in the Si sublattice relax. From studying plan-view and cross-sectional TEM samples in conjunction with simulated diffraction patterns, the three-dimensional structures of vacancy ordering were determined. The vacancy ordering structures are expected to exert a strong influence on the physical properties of epitaxial rare-earth silicide nanowires grown on (001)Si. © 2003 American Institute of Physics.