In-situ transmission electron microscopy has been used to study the deposition of Ni on clean Si surfaces and reaction to form NiSi2. The as-deposited structure and annealing behaviour is entirely different on (111) and (100) surfaces. On Si(111), the initial as-deposited layer appears to have the type-B NiSi2 structure. For Ni coverages above ~10 Å this is covered with polycrystalline fcc Ni. On annealing, if there is sufficient unreacted Ni and the total thickness is less than ~25 Å, the metastable hexagonal phase θ-Ni2Si is formed, which in turn converts to type-A NiSi2 on further annealing. For comparable coverages on Si(100), unreacted Ni transforms directly to NiSi2 during annealing. These results and others on the detailed evolution provide explanation for the microstructure of both (100) and (111) NiSi2 films, particularly the type-A/type-B thickness-dependent template phenomenon. In general, our results indicate the importance of the thickness and orientation dependence to the free energy of very thin films due to the significant fraction of interfacial atoms.