We conducted a first-principles study of the Debye-Waller factor for amorphous silicon (a-Si) using lattice-dynamical calculations in the harmonic approximation and direct ab initio molecular dynamics simulations using density-functional theory. By employing the harmonic approximation, we examined the effects of temperature on the diffraction maxima and the mean-square displacement (MSD) of silicon atoms in a-Si, considering the factors such as bond-length disorder, the presence of coordination defects, and microvoids in the a-Si networks. We observed a notable variation in atomic displacements between tetrahedrally bonded Si atoms and their dangling-bond counterparts originated from isolated or vacancy-induced clustered defects, including those associated with microvoids. The presence of defects led to an asymmetric non-Gaussian tail in the distribution of atomic displacements. Furthermore, considering temperature-induced anharmonicity at high temperatures, our study revels minimal impact of the anharmonic effects on the vibrational motion of Si atoms, at least within the context of our DFT calculations, for temperatures below 400 K. This analysis provides valuable insights into the vibrational properties of a-Si, offering a comprehensive understanding of vibrational behavior of Si atoms under different conditions.