CdTe/GaAs(001) heterostructures were fabricated by molecular beam epitaxy on chemically etched and thermally deoxidized GaAs(001) substrates, as well as GaAs(001) (3×1) buffer layers grown in situ by molecular beam epitaxy. Different growth protocols were also explored, leading to Te-induced (6×1) or (2×1) surface reconstructions during the early growth stage. High-resolution cross-sectional transmission electron microscopy was used to examine the final interface structure resulting from the different substrate preparations, and surface reconstructions. The (2×1) surface reconstruction led to pure (001) growth, while the (6×1) reconstruction led to an interface which included small (111)-oriented inclusions. In addition, deposition on etched and deoxidized GaAs(001) wafers led to preferential CdTe growth within etch pits and resulted in a macroscopically rough interface region.