Density functional perturbation theory, implemented within the projector augmented-wave method, is applied to a set of molecules (N2, O2, F2, CO, H2O, BF3, and SiF4) and to two solids (Si, GaAs). The results are compared to those obtained by the ultrasoft pseudopotential method. For the present systems, the two methods give similar vibrational frequencies, with differences below a few cm−1.