Background Quantifying the burden of diabetes mellitus is fundamental for managing patients in health service delivery systems and improves the understanding of the importance of prevention and early intervention of diabetes. In Switzerland, epidemiological data on diabetes are very scarce. In this study we provide a first national overview of the current situation of diabetes mellitus in Switzerland as well as the development of the prevalence, incidence, mortality and costs between 2006 and 2011. Methods Using health care claims data of a large health insurance group, current epidemiology and costs were determined from a sample of adult enrollees in 2011. The identification of patients with diabetes was based on prescription data of diabetes related drugs using the Anatomical Therapeutic Chemical Classification as proxy for clinical diagnosis. We further evaluated changes in epidemiology and costs between 2006 and 2011. All results were weighted with census data to achieve an extrapolation to the Swiss general population level. Results A total of 920’402 patients were enrolled in 2011 and 49’757 (5.4%) were identified as diabetes cases. The extrapolated overall prevalence of diabetes in Switzerland was 4.9% (2006, 3.9%). The incidence was 0.58% in 2011 (2007, 0.63%). The extrapolated mortality rate was 2.6% with no significant change over time. Annual diabetes costs to the mandatory health insurance increased from EUR 5,036 per patient in 2006 to EUR 5’331 per patient in 2011. Conclusions This study shows a high medical and economic burden of diabetes. The prevalence and costs of diabetes in Switzerland increased substantially over time. Findings stress the need for public health strategies to manage patients with chronic conditions and optimize resource allocation in health service delivery systems.