Phase formations in Co thin films (200angstrom in thickness) reacting with atomically clean Si(100), Ge(100), and Si0.80Ge0.20 epitaxial layer (800angstrom in thickness on Si(100) substrates) in UHV have been investigated. For the Co/Si system, it is found that CoSi (FeSi structure) is formed at 375°C through a very disordered CoSi phase, and the final CoSi2 phase is formed at 575°C. On the other hand, the Co5Ge7 phase was identified for the Co/Ge samples annealed at 300°C and 450°C and the final CoGe2 phase is formed at 600°C. For the Co/Si0.8Ge0.20 samples annealed from 400°C to 600°C, Co(Si1-yGey) phases with yapprox.0.10 were detected, and for annealing at 700°C, only the CoSi2 phase was formed. These results indicate a preferential Co-Si reaction when annealing the Co/SiGe structure. It was also found that the sheet resistance of the reacted thin films depend strongly on annealing temperature.