The atomic structures and the Schottky barrier heights of single crystal silicide–silicon interfaces were studied. Epitaxial NiSi2 and CoSi2 were grown under ultrahigh vacuum conditions on (111), (100), and (110) surfaces of Si. Lattice imaging by high resolution transmission electron microscopy allowed modeling of the interface atomic structures. Capacitance–voltage and current–voltage characteristics of these interfaces were studied. A dependence of barrier heights on orientation is observed which favors intrinsic mechanisms for their formation. The advantages of the present single crystal metal–semiconductor interfaces over the usual polycrystalline junctions in the study of Schottky barrier formation are demonstrated.