BACKGROUND: The Swiss national guidelines for the prevention of cardiovascular events have been published in 2005 by the Swiss Society of Cardiology (SGK) and the working group on lipids and atherosclerosis (AGLA). An agreement for global cardiovascular risk assessment and indications for cholesterol lowering among the international (IAS-AGLA) and the European (ESC score) guidelines is unknown. MATERIAL AND METHODS: Subjects aged >or=45 years were recruited using newspaper announcements for the participation in our free of charge cardiovascular prevention program of the Vascular Risk Foundation (Varifo). The data served to calculate cardiovascular 10 year risk and to compare IAS-AGLA und ESC score with respect to risk and lipid lowering indications. RESULTS: The primary prevention group included 713 subjects aged 55 +/- 6 years of which 47% were women. The mean 10-year risk +/- standard deviation was low (IAS-AGLA: 3.9% +/- 4.4% for myocardial infarction; ESC score: 1.7% +/- 1.8% for cardiovascular death). In those subjects qualifying for a lipid lowering intervention, according to the IAS-AGLA score or the ESC score, the percentage of agreement between both scores was only 18% (kappa value 0.31 [95%CI: 0.22-0.39], p < 0.0001). CONCLUSIONS: Our study shows, that the agreement for the available Swiss guidelines (IAS-AGLA, ESC score) for initiation of a lipid lowering therapy is low in our primary prevention group of subjects aged 45-65 years. According to the PROCAM study, about 30% of myocardial infarctions occur in persons with an intermediate risk. Therefore an improved risk stratification strategy is necessary.