High-quality CoSi2(100) layers in the thickness range of 200 to 500 Angstrom are formed by reactive deposition epitaxy. A model is described in which the deposition rate and substrate temperature are crucial in determining the epitaxial nature of the silicide. It is shown that good CoSi2/Si(100) alignment is only achieved when using low deposition rates (in the order of 0.1 Angstrom/s or less) combined with relatively high substrate temperatures during deposition(similar to 600 degrees C). At higher rates and/or lower temperatures, a fraction of misoriented CoSi2 grains is formed. A study of the crystalline quality of the CoSi, layers as a function of Co flux and deposition temperature is presented, and special attention is devoted to the thermal stability of the layers during high temperature annealing.