Quasi-phase-matched waveguides are known to degrade when generating high intensity short wavelength light. Photoinduced changes in the refractive indices can lead to reduced efficiency by broadening phase-matching curves or inducing power dependent losses. In this work a pump-probe technique was used to investigate photorefractive effects in nonlinear optical waveguides. A strong two photon photorefractive effect in single domain and Ti-poled LiNbO3 was found that is considerably reduced in electric field periodically poled LiNbO3 and is absent in Rb-exchanged KTiOPO4.