The influence of amorphization of the Si substrate by Ge+ implantation on the microstructural evolution of CoSi2 thin films has been investigated by transmission electron microscopy (TEM), X-ray diffraction (XRD) and four-point-probe measurement. While the silicide films formed on unimplanted or recrystallized Si were similar in formation kinetics, microstructure and resistivity, unique features were found for silicide films formed on amorphized Si. The phase transformation to CoSi2 on amorphized Si was considerably accelerated, the silicide grain size was smaller, and the CoSi2/Si interface was much smoother on the amorphized Si. Direct evidence of grain boundary diffusion induced silicide/Si interface roughness was obtained. The origin of the difference in both the microstructure and kinetics on different Si substrates is explained by the latent energy stored in amorphous Si, increasing the silicide nucleation rate. Weak XRD peaks and different texture were found for the CoSi2 formed on amorphized Si. The facts that the dominant diffusing species during CoSi2 formation is Co, and the new phase was developed in an amorphous medium are thought to be responsible for these phenomena.