We have measured the band offsets and materials properties of epitaxial SrTiO3/Si(001) heterojunctions for both n and p substrates, with and without an interfacial SiO2 layer. The through-air transfer from the growth chamber to the photoemission system results in significant surface hydroxylation and roughening, although the SrTiO3-Si interface is undisturbed. Surface hydroxylation notwithstanding, the structural quality of 20 Angstrom thick epitaxial SrTiO3 on Si(001) is comparable to that of bulk SrTiO3(001). We find valence and conduction band offsets of similar to2.1 and similar to0.0 eV, respectively, independent of doping type and the presence of SiO2. These results are consistent with theoretical band offset predictions based on the electron affinity rule, modified by the presence of an interface dipole.