We show that the HF acid etch commonly used to prepare SrTiO3(001) for heteroepitaxial growth of complex oxides results in a non-negligible level of F doping within the terminal surface layer of TiO2. Using a combination of x-ray photoelectron spectroscopy and scanned angle x-ray photoelectron diffraction, we determine that on average â 13% of the O anions in the surface layer are replaced by F, but that F does not occupy O sites in deeper layers. Despite this perturbation to the surface, the Fermi level remains unpinned, and the surface-state density, which determines the amount of band bending, is driven by factors other than F doping. The presence of F at the STO surface is expected to result in lower electron mobilities at complex oxide heterojunctions involving STO substrates because of impurity scattering. Unintentional F doping can be substantially reduced by replacing the HF-etch step with a boil in deionized water, which in conjunction with an oxygen tube furnace anneal, leaves the surface flat and TiO2 terminated.