Background: The Swiss hepatitis C cohort (SCCS) began recruiting in September 2000 with the aims of clarifying factors associated with disease progression, identifying optimal standardised treatment regimes for patients and supplementing national epidemiological information of the Swiss Federal Office of Public Health (SFOPH). Methods: Adults with hepatitis C infection (HCV), aged 18 years or over were recruited into the cohort from centres across Switzerland with prospective data collection at enrolment and subsequent follow-up visits. We described baseline characteristics of the cohort, compared selected variables with national surveillance data from the SFOPH, and analysed progression to a diagnosis of primary hepatocellular carcinoma (HCC) or death from liver cancer. Results: A total of 2452 participants were enrolled in the cohort between 1 September 2000 and 31 December 2005, contributing a total of 4239 person years of follow-up. Similar to national surveillance data, participants were 63% male, 75% Swiss nationals, had a median age at enrolment of 42 years and 57% had a history of injection drug use. Twenty-four % had elevated alanine aminotransferase and 14% were cirrhotic. For cirrhotics, the rate of death from liver cancer or of developing a primary HCC was 4.0 per 100 person-years; 4.8 (95% confidence interval: 2.8 - 8.2) times higher than for non-cirrhotics. Conclusion: This multi-centre cohort successfully enrolled a broad spectrum of HCV-infected persons in Switzerland and will, in future, provide nationally generalisable results on the progression of HCV-infection and associated diseases in Switzerland.