The origin of the superstructure observed in epitaxial yttrium oxide (Y2O3) layers on Si (001) is determined by electron energy loss spectroscopy (EELS). The oxygen K edge is measured both in the superstructure and a defect-free region of the Y2O3 layers and they are compared to EELS spectra obtained from bulk stoichiometric and reduced Y2O3. It is shown that as a result of the epitaxial growth, oxygen vacancies order into a superstructure creating nonstoichiometric regions in an otherwise stoichiometric Y2O3 layer. Furthermore, it is shown that oxygen deficiency introduces a change of the density of states of the lower conduction band of Y2O3. © 2003 American Institute of Physics.