Molecular beam epitaxy has been used to grow heteroepitaxial CuInxSey layers on Si and GaAs substrates. Layers of different Cu/In ratios have been grown to study the formation of different phases such as CuInSe2 chalcopyrite (alpha-phase) and defect-chalcopyrite/stannite phases (beta-phase) in this material system. A variety of characterization methods are used to identify if the layer is a single phase compound or a mixture of two compounds. Structural and optoelectronic properties strongly depend on the Cu/In ratio. Epitaxial layers with an ion channeling yield of 7% and an X-ray rocking curve width of about 770 arcsec have been grown. Linear and planar defects as well as interdiffusion of elements are expected in the interfacial region due to layer-substrate mismatch and growth conditions. These defects have been identified with high resolution transmission electron microscopy. The chemical composition of the interfacial layer has been investigated by Rutherford backscattering spectroscopy, microprobe energy dispersive X-ray analysis and X-ray diffraction. An interfacial CuSexSiy layer is formed during the growth of CuInxSey on Si. In the case of GaAs substrates, Ga from the substrate diffuses into the CuInxSey and a quaternary compound Cu(In,Ga)(x)Se-y is formed at the interface.