In the present work, CoSi2 films with good crystallinity were prepared on Si (100) substrate by a two-step method. This method includes an epitaxial growth of Co films on the Si (100) substrate, and in-situ annealing of the Co/Si him in vacuum. First, Co films were deposited on Si (100) substrate by electron beam evaporation with the substrate temperature ranging from room temperature to 360 degreesC. The structure of these Co/Si films was characterized by cross-sectional transmission electron microscopy (XTEM) and atomic force microscopy (AFM). It has been found that when deposited on substrate at temperatures below 360 degreesC, Co polycrystalline films are formed with an average grain size less than 30 nm. However, when raising the substrate temperature to 360 degreesC, fee cobalt film grows epitaxially on the Si (100) substrate. The epitaxial orientation is (001) Co//(001) Si, [100] Co//[110] Si as determined from the electron diffraction results. AFM images of such film show many square facets on the surface of the Co films, the average size of these facets being approximately 100 x 100 nm. The epitaxial Co films were annealed in situ under vacuum at temperatures ranging from 500 degreesC to 600 degreesC. The Co film reacted with Si substrate and was transformed into CoSi2. The crystalline quality of the CoSi2 films was found to be improved compared with CoSi2 films prepared using polycrystal precursors.