BACKGROUND AND OBJECTIVES: The Swiss HIV Cohort Study (SHCS) was initiated in 1988 and represented the main scientific component of the comprehensive response to the AIDS epidemic in Switzerland. It brought together physicians and scientists from five university hospitals (Basel, Berne, Geneva, Lausanne and Zurich) and two Cantonal hospitals (Lugano and St. Gallen). The objective of SHCS was, and still is, to produce rapid, high quality patient-oriented medical research in the field of HIV infection. METHODS: SHCS is a prospective population-based cohort study. Any HIV-infected person aged > or = 16 years is eligible to participate. Data collection and study procedures are standardised. Data quality and protocol monitoring are conducted at the coordination and data centre in Lausanne. Detailed information on demographics, income, mode of HIV acquisition, risk behaviours, clinical events, laboratory results, treatment and treatment tolerance is collected at registration and at 6-monthly intervals. RESULTS: Since 1996, 10,600 persons have been enrolled and the SHCS study population is considered fairly representative of the HIV-infected population in Switzerland, at least in terms of gender and mode of HIV acquisition. In 1999, 4600 patients were actively followed up and more than 70% of patients were receiving highly active antiretroviral therapy (HAART). As a consequence, mortality and the incidence of HIV-related opportunistic infections have decreased significantly in the recent past. Between 1996 and 2000, 91 original manuscripts have been published by SHCS scientists and physicians, almost exclusively in peer-reviewed journals. A wide range of scientific questions have been addressed, including HIV primary infection, the natural history of HIV infection, the clinical and biological impact of HAART, drug resistance, risk factors for disease evolution including the timing of treatment initiation, the role of CD4 receptors, the validity of HIV surveillance reports, determinants of treatment access and tolerance, clinical trials of new drug combinations, the interruption of prophylaxis following a favourable response to HAART and issues relating to quality of life and interaction between income, social level and disease evolution. CONCLUSION: The SHCS has had, and continues to have, a significant impact on medical practice, public health and research in Switzerland and beyond. It represents a network of excellence which has brought together and fostered intensive collaboration between physicians and institutions throughout this country and beyond. This was possible thanks to the support of the Federal Office of Public Health and the commitment of primary care physicians, researchers and patients. This project may be model for focused and prioritised multicentre and transdisciplinary research programmes.