We measured the low temperature internal friction of a variety of hydrogenated amorphous, nanocrystalline, polycrystalline, and epitaxial silicon thin films. Most of the films studied are prepared either by hot-wire chemical-vapor deposition (HWCVD) or by plasma-enhanced chemical-vapor deposition (PECVD). We show that structural changes with varying modes of deposition can be monitored by the internal friction measurements, which are a sensitive probe to structural disorder resulted from atomic tunneling states below 10 K. For hydrogenated amorphous silicon films, the measurements are also sensitive to the content of atomic hydrogen and bulk molecular hydrogen trapped in the films. With H 2 dilution of the silane during deposition, a transition from amorphous to nanocrystalline phase takes place as H 2 dilution increases. We show that with increasing volume of nanocrystallinity, the internal friction increases in contrast to our common expectation. The results suggest a large structural disorder in the nanocrystalline phase that is at least comparable to that of amorphous phase exists. The observation of internal friction peaks in amorphous HWCVD films and in nanocrystalline PECVD films indicates that the microstructures of the HWCVD and PECVD films are different.