The crystal structure and interface structure of ultrathin cobalt disilicide films, prepared on a Si(001) substrate at 400 °C, have been examined using transmission electron microscopy (TEM). Analysis of the electron diffraction data reveals that there are three general types of epitaxy between the silicon substrates and the cobalt disilicide films: (1) CoSi2(110)//Si(001), CoSi2[001]//Si[110]; (2) CoSi2(110)//Si(001), CoSi2[1̄10]//Si[110]; and (3) CoSi2(001)//Si(001), CoSi2[110]//Si[110]. Using cross-sectional high-resolution TEM for all three types of epitaxy showed that (1) the cobalt disilicide films form an ultrathin flat layer and (2) the interface between the substrate and the film is abrupt with an atomic level for all three types of epitaxy. Dark-field observations also revealed unique localized distributions of three different types of crystalline domains. The domains of CoSi2(110) had elliptic and those of CoSi2(001) had round shapes that were several hundred nanometers in diameter. Each domain consisted of small crystalline epitaxial particles approximately 5–30 nm in diameter as well as an amorphous phase consisting of a cobalt disilicide crystal structure characterized by short-range order.