The agglomeration of Co silicide films formed on Si substrates processed with different Co film thickness was investigated by TEM, XRD, and four-point-probe measurements. It was found that thermal grooving always accompanies the film formation, while islanding can occur during high temperature thermal stability testing, or during formation of very thin films at moderate temperatures. In addition to whole film agglomeration, partial agglomeration on the top of the film has been observed, which is prominent and important for thin films. A theoretical model of agglomeration for silicide films is presented, which shows that when the ratio of grain size to film thickness is smaller than a critical value, the film will not lose its continuity. Also, grain boundary migration was found to have a suppressing effect on thermal grooving. Both a small grain size and a low grain boundary energy are shown to be favorable for improving the thermal stability.