The interaction of thin films of amorphous NiNb alloys with Si(001) is studied by TEM. It is found that the relaxation of internal stresses in films strongly influences the subsequent formation of silicides. At the initial stage the formation of nuclei of silicides in the amorphous film close to the interface leads to the local stress relaxation that is followed by an enhanced formation of Nisi2 and NbSi2 grains. At the later stage the reaction may result in the crystallization of the film and in the appearance of Ni flow into the Si substrate followed by the formation of Nisi2 epitaxial islands. Structure and configuration of Nisi2 islands are studied. It is shown that the formation of silicides in the reaction of NiNb films with Si depends on various factors and cannot be completely reproduced in different experiments. The role of the native SiO2 layer is discussed.