After publication of the "Good Practice Secondary Data Analysis" (GPS) in 2005, the scientific use of secondary data has further increased. Based on several feedbacks to the first version of this guideline, the Working Group "Collection and Use of Secondary Data" (AGENS) of the German Society of Social Medicine and Prevention (DGSMP) together with the working group 'Epidemiological Methods' of the German Society of Epidemiology (DGEpi), the German Society for Medical Informatics, Biometrics and Epidemiology (GMDS) and the German Society of Social Medicine and Prevention (DGSMP) undertook the first revision of the GPS, which will be implemented in the beginning of 2008. The second version of the GPS was restructured in relation to the first version. Now, the numbering of the guidelines is the same as that of the Good Epidemiological Practice (GEP). The GPS guidelines also have the same wording as in the GEP. The specific conditions and requirements of secondary data analysis were addressed in the explanations of the guidelines and their recommendations. The glossary at the end of the GPS was extended. In the last three years the GPS has become established as a standard for secondary data analyses. Additionally, the GPS may be used as a basis for contractual arrangements between data owners and researchers. This version of the GPS is valid to the end of 2010.