The surface layers formed in LiNbO3 waveguides, fabricated by Zn diffusion from the vapor phase, have been investigated by time of flight elastic recoil detection analysis using 127I ions. The key features of this technique, simultaneous profiling of all ions and a depth of analysis ≪1 μm, have allowed a detailed and quantitative characterization of the surface layers. The Zn diffusion into LiNbO3 can be understood as a 2Li↔Zn exchange process. As a consequence, an outermost layer of several hundreds of nanometers is formed, consisting of LiNbO3 and ZnNb2O6 phases showing complementary profiles. A good correlation has been found between the composition profiles and the optical waveguiding behavior. After thermal annealing of the waveguides, a thinner layer containing a uniform mixture of ZnO and LiNbO3 is generated followed by a transition to a graded solid solution of Zn into LiNbO3. © 2002 American Institute of Physics.