A quantitative comparison of the photorefractive effect in annealed proton-exchanged channel waveguides in MgO-doped and congruent LiNbO3 at the wavelengths of 633 and 830 nm is presented. An accurate measurement technique is described to measure the refractive-index change as a function of time and the guided mode intensity for different wavelengths. The results show that doping with 7% MgO reduces the photorefractive effect at a wavelength of lambda = 633 nm by 2 orders of magnitude. The photorefractive effect in the doped substrate shows only a weak dependence on the guided power. Doping with 4 mol.% MgO has only little effect on the photorefractive effect compared with that on the congruent material. A reduced photovoltaic current is responsible for the small photorefractive effect in the 7 mol.%-doped substrate.