Transplantation medicine has evolved from an experimental approach to a life saving standard treatment option for many patients. Each year, 400 solid organ (kidney, heart, lung, liver, pancreas and Langerhans islets) and 100 allogenic stem cell transplants are performed in six Swiss transplant centers (Basel, Bern, Geneva, Lausanne, Zurich and St. Gall). Following transplantation, life long pharmacological immunosuppression is required to control rejection. These treatments favor the development of infections and malignancies, which together with uncontrolled rejections are responsible for the majority of deaths. In order to coordinate and promote research in the field of transplantation including psychosocial aspects all Swiss transplant centers have agreed to establish a Swiss Transplant Cohort Study (STCS) financed by the Swiss National Research Foundation. This interfacultary and interdisciplinary effort will create the first nation-wide transplantation cohort in which all types of transplanted organs are included. It will allow studies aiming at improving patient survival and quality of life. Data interrelated to infectious problems, immunosuppression, graft function, psychosocial aspects and patient survival, as well as patient specimens will be collected prospectively in a longitudinal manner at specific time points. The design of the STCS is in accordance with the new transplantation law, where other requirements such as quality assurance are foreseen. All hospitals with transplant centers further financially support the STCS. Since fall 2006, transplant experts from all six Swiss transplant centers have collaborated to establish the various datasets of the STCS. Thanks to the common effort all the different datasets for each organ are presently finalized. The possibility of coexisting transplants performed at various time points, double transplants and retransplants in a single patient introduces a high degree of complexity in the STCS and requires a sophisticated information flow. Specialists in epidemiology, informatic technology and transplantation medicine are presently elaborating the codebooks and various formularies of the future web based information capture system. So far the milestones initially planned have been respected and it is planned to include the first patients in January 2008.