We demonstrate that CoSi₂ directly grows epitaxially on H-terminated Si(001) and the interface is atomically flat. The hydrogen present on the Si surface seems to suppress the direct reaction of Co with Si up to ∼400^oC. Thus, the hydrogen at the Co/Si interface hinders the formation of low temperature (metal-rich) phases such as Co₂Si and CoSi. Upon thermal desorption of hydrogen at around ∼460^oC, the direct epitaxial growth of CoSi₂ on Si(001) occurs. However, with the increase of initial Co film thickness, cracks are formed partially due to a strong tensile stress. More detailed study is needed concerning the effects of such defects for the practical applications to VLSI.