The early stages of the nucleation and growth of nickel silicides in Ni-Si multilayers evaporated onto oxide-stripped <100> Si substrates and annealed at 150 °C have been studied by cross-section transmission electron microscopy (TEM). Observed differences in the interaction of evaporated Ni with amorphous silicon and single crystal <100> Si have been explained by thermodynamic modeling of the Ni-Si system. The as-deposited films show a 3 nm amorphous Ni-Si intermixed layer at all Ni-Si interfaces, including that with the single-crystal Si substrate. Crystalline Ni2Si formed in all annealed films, consuming the elemental Ni layers. The amorphous alloy layer grows concurrently with Ni2Si during the reaction with a-Si; however, there is no amorphous phase present at the Ni2Si - <100> Si interface. Thermodynamic calculations show that at 150 °C metastable equilibrium might be expected between a-Si, the amorphous phase, and Ni2Si; but not between Ni2Si, the amorphous phase, and crystalline Si. The composition of the amorphous phase is very close to a-Ni50Si50. After a 6 hour anneal at 150 °C, crystalline NiSi forms between the a-Si and the Ni2Si layers by crystallization of the amorphous phase. Further annealing is necessary to form NiSi at the <100> Si - Ni2Si interfaces.