Proton‐exchanged waveguides fabricated in LiNbO3doped with 4.5% MgO and 0.1–0.2 % Nd:4.5% MgO have been characterized by prism‐coupling and infrared‐absorption spectroscopy. Single and multimode doped waveguides have temporally stable effective mode indices, and the refractive‐index profiles are identical to those observed for proton exchange in congruent LiNbO3. Effective diffusion coefficients for proton exchange in dopedxandz‐cut substrates have been estimated for waveguide‐fabrication temperatures in the range 182–235 °C. While diffusion coefficients for MgO:LiNbO3and Nd:MgO:LiNbO3appear to be identical, waveguides formed in the doped substrates have substantially smaller diffusion coefficients compared to waveguides formed in congruent LiNbO3, the magnitudes being down by as much as 50% forx‐cut waveguides and 37% forz‐cut waveguides. These results should prove of value when using the proton‐exchange technique to design waveguide lasers in Nd:MgO:LiNbO3.