The relationship between deformations of crystal lattice and extraordinary refractive index change has been experimentally determined for proton-exchanged lithium niobate waveguides. It has been shown that the strains induces by the substrate strongly modifies the phase diagram obtained for powders. Depending on exchange and annealing conditions and crystal cuts, at least the six phases x -, 13-, -, 5-, ( and 'Ti - HxL:L1-NbO3 can exist in single crystal layers. The regularities of proton exchange in lithium niobate crystals under different exchange and annealing conditions are studied and various specific features are explained.