Morphological evolution associated with silicidation of Co thin films deposited on (100) and (111) Si substrates has been followed using transmission electron microscopy with in situ thermal annealing from ambient temperature up to 850°C. Noticeable structural changes associated with the formation of CoSi2 occur at temperatures as low as 400°C and the reaction is essentially complete at about 500°C. Prolonged heating above 500°C leads to CoSi2 grain growth and coalescence and, finally, to pinholes formation. Silicidation of Co films on (100) and (111) Si substrates follows the same pattern. The morphology of films annealed in situ is similar to those annealed ex situ except that the Si/CoSi2 interface appears to be much rougher. This behavior is associated with the specific geometry of cross-sectional TEM specimens, where surface diffusion dominates bulk diffusion. Very thin Co films, which have less contribution from surface diffusion than thicker films, are ideal for studying dynamic phenomena at Co/Si reactive interfaces.