Waveguides fabrication in Z- and X-cut LiNbO3 crystals by vapor zinc diffusion has been studied by secondary ion mass spectrometry and optical measurements. Compositional analysis of diffused substrates shows the formation of a Zn rich superficial layer, followed by a deeper region with decreasing Zn concentration. A subsequent thermal annealing process has been performed to let zinc ions further diffuse into the substrates. The composition profiles have been correlated with the refractive index profiles, reconstructed by optical reflectivity measurements. The results and the nature of the detected layers are discussed and correlated with previous x-ray studies obtained in the same samples.