In recent years, ultrashort laser pulses have drawn increasing interest for the direct writing of photonic structures into different materials. Several optical devices have already been demonstrated, e.g. optical waveguides, waveguide amplifiers and lasers, beam splitters, couplers, stacked waveguides and three-dimensional waveguide arrays and gratings. The investigations were mainly focused on glasses where the laser irradiation causes a rise in refractive index. However, for different applications the realization of waveguides in crystalline media is interesting. Here, we present investigations on femtosecond laser induced modifications in crystalline quartz. We show that the irradiation leads to a refractive index decrease which is due to amorphization of the focal volume. A detailed analysis of the structures is performed with transmission electron microscopy and X-ray diffraction and topography. Our investigations show that the irradiated amorphous core creates a stress field in the surrounding material that possesses a positive index change and therefore supports the guiding of light. The results of the X-ray experiments allow a quantitative characterization of the stress field. We are able to simulate the stress distribution by a simple model based on the density difference between the amorphous and crystalline material. From this the refractive index profile can be calculated and compared to experimental results. The light guiding properties of the compressed regions and the fact that only one polarization is guided can be verified by the simulation results.