We have examined the effects of annealing in air at 350 to 550 degree(s)C on proton-exchanged waveguides in lithium niobate crystals. By making a complex analysis of the processes that take place during annealing, which included structural, waveguiding-optical, IR-spectroscopical, and thermogravimetric measurements, we were able to find the conditions under which the LiNb3O8 phase is formed in H:LiNbO3 waveguides. A noticeable increase of LiNb3O8 begins at the moment the refractive index increment at the boundary of the initial proton-exchanged waveguide reaches the value (Delta) ne equals 0.037. With further annealing, when the (Delta) ne on the surface of the plate also becomes equal to 0.037, there begins the evaporation of Li2O and intensive formation of LiNb3O8. The results presented enable one to understand why under certain conditions of annealing the optical losses in H:LiNbO3 waveguides become greater, and to optimize the conditions of such annealing to produce high-quality waveguides.