X-Shooter is the first 2nd generation instrument to be installed at Paranal early 2008. It is a single target spectrograph covering in a single exposure a wide spectral range from the UV to the K' band with maximum sensitivity. Another key feature of the instrument is its fast response, obtained by making it simple and easy to operate. Compared to other big VLT instruments X-Shooter has a relatively small number of moving functions, but nevertheless the requirements on the whole instrument software are quite demanding. In order to cover the wide spectral range with high efficiency, the instrument is split into three different arms, one being cryogenically cooled. The high level coordinating software architecture provides all the facilities for parallel operation with the maximum achievable level of synchronicity. Low level X-Shooter requirements are also quite stringent, since to compensate for slit misalignments among the three arms, an active piezoelectric actuator system is envisaged. The low-level architecture, besides the typical control of single devices (like motors, sensors and lamps), handles the required real-time operations. The software integration and test is also an issue, being X-Shooter a collaborative effort among several institutes spread around Europe. The whole instrument software architecture is presented here, entering in details into its main modules such as the instrument control software, the observation software and the observing templates structure and their integration in the VLT software environment.