The selective formation of TiSi2 using low-pressure chemical vapor deposition on Si (001) substrates has been studied with emphasis on the first nucleating phases and the polymorphic transition of the silicide. It was found that C49-TiSi2 with a few C54-TiSi2 grains was the first nucleating phase. Most of the C49-TiSi2 grains are epitaxially formed on the substrate with limited silicon consumption. The further growth of epitaxial silicide occurs by accommodation of atoms at the ledge provided by a spiral terrace. However, the C54-TiSi2 grains were formed with a large amount of silicon consumption. The C54 grains acted as a point source for the polymorphic transition. The TiSi2 was selectively deposited even on a contact-patterned substrate, in which the exposed Si surface is extremely limited, so that a self-aligned plug was formed. However, the substrate consumption and the phase of the silicide were strongly affected by the dopant type of the substrate. The crystallinity and its structural relationship with the substrate were verified using X-ray diffraction and transmission electron microscopy.