The layer reversal phenomenon of the cobalt/zirconium (Co/Zr) bilayer during rapid thermal annealing (RTA) and the epitaxial growth of a cobalt disilicide (CoSi2) layer have been investigated. The interlayed Zr layer effectively limited the flux of Co atoms by forming the Co-Zr intermediate phase and the Zr-O (or Zr-N) compound as well as effectively removing the native oxide formed on the Si substrate which interferes with the direct Co-Si interaction. Below 600 degrees C, the Co-Zr intermediate alloy with ZrO2 (i.e., Co-Zr-O) were formed without any silicide formation of cobalt. However, the layer reversal occurred after RTA above 700 degrees C, resulting in the epitaxial CoSi2 formation on (001) Si substrate. The CoSi2 layer improved with increasing temperature, so that both the interface of the Zr-Co-Si alloy layer/CoSi2 and the CoSi2/Si were extremely smooth after RTA at 900 degrees C.