The X-shooter data reduction pipeline, as part of the ESO-VLT Data Flow System, provides recipes for Paranal Science Operations, and for Data Product and Quality Control Operations at Garching headquarters. At Paranal, it is used for the quick-look data evaluation. The pipeline recipes can be executed either with EsoRex at the command line level or through the Gasgano graphical user interface. The recipes are implemented with the ESO Common Pipeline Library (CPL). X-shooter is the first of the second generation of VLT instruments. It makes possible to collect in one shot the full spectrum of the target from 300 to 2500 nm, subdivided in three arms optimised for UVB, VIS and NIR ranges, with an efficiency between 15% and 35% including the telescope and the atmosphere, and a spectral resolution varying between 3000 and 17,000. It allows observations in stare, offset modes, using the slit or an IFU, and observing sequences nodding the target along the slit. Data reduction can be performed either with a classical approach, by determining the spectral format via 2D-polynomial transformations, or with the help of a dedicated instrument physical model to gain insight on the instrument and allowing a constrained solution that depends on a few parameters with a physical meaning. In the present paper we describe the steps of data reduction necessary to fully reduce science observations in the different modes with examples on typical data calibrations and observations sequences.© (2010) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.