In this study, cross-sectional transmission electron microscopy (XTEM) was used to investigate the defect structure which occurs at the interface between CdTe(001) and GaAs(001). The heterostructures were fabricated by molecular beam epitaxy on chemically etched and thermally deoxidized GaAs(001) substrates as well as GaAs(001) buffer layers grown in-situ by molecular beam epitaxy. This allowed for investigation of the GaAs surface preparation on the subsequent interfacial structure. The as-etched substrate led to a microscopically rough interface with the CdTe depositing in etch pits on the GaAs surface, while growth on the buffer layer led to a macroscopically flat interface. Further, growth was accomplished on different Te-induced surface reconstructions ((6×1) vs (2×1)) in an effort to understand the role of the precursor surface treatment on the subsequent interfacial structure. In this case growth on the (6×1) reconstruction led to the introduction of (111)-oriented inclusions at the interface, while the (2×1) reconstruction led to pure (001)-oriented growth. A mechanism for the formation of planar defects at the CdTe/GaAs(001) interface is described which is based on local misorientations of the CdTe and GaAs. Finally, preliminary results of ex-situ annealing experiments on the interfacial defect structure will be discussed.