We report measurements of site-to-site diffusion in proteins, using frequency-domain measurements of time-dependent energy transfer. The possibility of such measurements is shown from simulations which demonstrate that donor-to-acceptor (D-to-A) diffusion alters the donor frequency response, and that this effect is observable in the presence of a distribution of distances. For decay times typical of tryptophan fluorescence, the simulations indicate D-to-A diffusion coefficients can be measured ranging from 10-7 to 10-5 cm2/s. This possibility was verified by studies of a methylene-chain linked D-A pairs in solutions of varying viscosity. D-to-A diffusion was also measured for acceptor-labeled melittin in the random coil and α-helical states. Unfolding of troponin I results in increased D-A diffusion. Surprisingly, more rapid diffusion was observed for melittin in the α-helical state, but over a limited range of distances.