The epidemiological situation in Switzerland was characterised by a substantial decline in the number of AIDS cases and HIV-related deaths following the introduction of highly active antiretroviral therapy (HAART). The number of new HIV infections, has, however increased in recent years and AIDS cases and related deaths are no longer declining. We discuss three examples of issues that are relevant to epidemiology and public health in order to illustrate the importance of the study in this context: (i) use of SHCS data to inform the interpretation of routine surveillance data based on reports from physicians and laboratories to the Federal Office of Public Health (FOPH); (ii) analyses of access to and utilization of HAART across different groups of study participants, including migrant populations, those with lower socio-economic status and patients infected through intravenous drug use; and (iii) the monitoring of trends in self-reported sexual behaviour, including condom use with stable and casual partners. The examples demonstrate that the study is an important resource for epidemiological analysis and public health surveillance and action in Switzerland.