We present a detailed study of the structure and hydrogen bonding in silicon thin films ranging from amorphous to microcrystalline. We emphasize the results for hydrogenated polymorphous silicon films obtained under plasma conditions close to powder formation where silicon clusters and nanocrystals contribute to growth. Fourier Transform Infra-Red (FTIR) spectroscopy, Raman spectroscopy, X-Ray-Diffraction (XRD), and hydrogen evolution measurements are performed to characterize the hydrogen bonding and the structure of the films in their as-deposited state and after isochronal annealing at increasing temperature in the range of 300 to 600 °C. While Raman spectroscopy and XRD give an average information on the structure of the films, without clear evidence of the presence of crystallites in the polymorphous films, infrared spectroscopy and hydrogen evolution measurements which probe the local hydrogen related structure are shown to be perfectly adapted to characterize polymorphous silicon films. In particular, IR spectroscopy measurements, reveal the presence of a stretching band at 2030 cm−1, associated with a peak at 873 cm−1 in the bending region and a downward shift in the Si-H wagging mode from 640 cm−1 to 622 cm−1. We attribute the 2030 cm−1 mode to the presence of hydrogen bonded at the surface of the plasma produced silicon clusters and nanocrystals. This assignment is supported by hydrogen evolution measurements in which a sharp low-temperature hydrogen evolution peak appears at around 420 °C followed by up to five peaks at higher temperatures. This particular hydrogen bonding in polymorphous silicon films is also supported by isochronal annealing studies which show that the bands at 2030 cm−1 and 873 cm−1 vanish at annealing temperatures corresponding to the low temperature hydrogen evolution peak. Based on these results and their correlation with the hydrogen-related material structure, we propose a picture for the structure of polymorphous silicon films that accounts for the observed features.