The early stages of the thermally induced epitaxial realignment of undoped and As-doped polycrystalline Si films deposited onto crystalline Si substrates were monitored by transmission electron microscopy. Under the effect of the heat treatment, the native oxide film at the poly-Si/c-Si interface begins to agglomerate into spherical beads. The grain boundary terminations at the interface are the preferred sites for the triggering of the realignment transformation which starts by the formation of epitaxial protuberances at these sites. This feature, in conjunction with the microstructure of the films during the first instants of the heat treatment, explains the occurrence of two different realignment modes. In undoped films the epitaxial protuberances, due to the fine grain structure, are closely distributed and grow together forming a rough interface moving toward the film's surface. For As-doped films, the larger grain size leaves a reduced density of realignment sites. Due to As doping some of these sites grow fast and form epitaxial columns that further grow laterally at the expense of the surrounding polycrystalline grains.