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Since it is now possible to record vibrational spectra at nanometer scales in the electron microscope, it is of interest to explore whether extended defects in crystals such as dislocations or grain boundaries will result in measurable changes of the phonon densities of states (dos) that are reflected in the spectra. Phonon densities of states were calculated for a set of high angle grain boundaries in silicon. The boundaries are modeled by supercells with up to 160 atoms, and the vibrational densities of states were calculated by taking the Fourier transform of the velocity–velocity autocorrelation function from molecular dynamics simulations with larger supercells doubled in all three directions. In selected cases, the results were checked on the original supercells by comparison with the densities of states obtained by diagonalizing the dynamical matrix calculated using density functional theory. Near the core of the grain boundary, the height of the optic phonon peak in the dos at 60 meV was suppressed relative to features due to acoustic phonons that are largely unchanged relative to their bulk values. This can be attributed to the variation in the strength of bonds in grain boundary core regions where there is a range of bond lengths.