Proton-exchangedLiNbO3optical waveguides(HxLi1−xNbO3)exhibit very complex structural behavior which is different from that known for their powders. Seven crystallographic phases have been identified in theHxLi1−xNbO3layers. A method to determine the proton concentration in different phases has been proposed. Correlation between the crystal structure, hydrogen concentration, and the ordinary and extraordinary refractive indices has been experimentally determined allowing one to explain some optical phenomena observed and to predict the characteristics of a great variety of proton exchanged waveguides. ©1997 American Institute of Physics.