The use of ultrashort laser pulses has found widespread attention in the microstructuring of transparent materials. Specifically, the origin of refractive index changes in glasses and crystalline materials was extensively investigated. In LiNbO 3 , which is an important material for nonlinear optical applications, the possibility of waveguide fabrication with fs laser pulses was also shown. Recently, two distinct types of waveguides were discovered in LiNbO 3 which show different thermal stability and optical properties. In one type, frequency doubling of 1064-nm radiation was demonstrated. Here, we discuss the different origins of the two waveguide types and present results of thermal annealing experiments. Furthermore, the influence of the processing parameters and the focussing on the properties of the waveguides was investigated. The electrooptic coefficient of the waveguide was measured and gives evidence that the nonlinear properties of the crystal are depleted by the laser structuring.