We report on investigations of the bulk microstructuring of lithium niobate crystals with intense femtosecond laser pulses. In different crystal cuts, optical waveguides were produced whose properties depend strongly on the processing parameters. To explore the origin of the refractive index changes, we subjected the crystals to different conditions (like temperature, illumination, etc.) while monitoring the waveguide output. This way several mechanisms for the change in refractive index could be singled out. These include the photorefractive effect, inhomogeneous ion concentrations and stress in the crystalline lattice. As an application, we demonstrate frequency doubling of 1064 nm laser radiation in a microstructured phase-matched waveguide. (c) 2007 Elsevier B.V. All rights reserved.