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Abstract Background Physical inactivity, unhealthy dietary habits, smoking and high alcohol consumption are recognized risk factors for cardiovascular disease and cancer. Web-based health risk assessments with tailored feedback seem promising in promoting a healthy lifestyle. This study evaluates the effectiveness of a web-based health risk assessment with individually-tailored feedback on lifestyle behaviour, conducted in a worksite setting. Methods/Design The web-based health risk assessment starts with a questionnaire covering socio-demographic variables, family and personal medical history, lifestyle behaviour and psychological variables. Prognostic models are used to estimate individual cardiovascular risks. In case of high risk further biometric and laboratory evaluation is advised. All participants receive individually-tailored feedback on their responses to the health risk assessment questionnaire. The study uses a quasi-experimental design with a waiting list control group. Data are collected at baseline (T0) and after six months (T1). Within each company, clusters of employees are allocated to either the intervention or the control group. Primary outcome is lifestyle behaviour, expressed as the sum of five indicators namely physical activity, nutrition, smoking behaviour, alcohol consumption, and symptoms of burnout. Multilevel regression analysis will be used to answer the main research question and to correct for clustering effects. Baseline differences between the intervention and control group in the distribution of characteristics with a potential effect on lifestyle change will be taken into account in further analyses using propensity scores. Discussion This study will increase insight into the effectiveness of health risk assessments with tailored feedback and into conditions that may modify the effectiveness. This information can be used to design effective interventions for lifestyle behaviour change among employees. Trial registration Dutch Trial Register NTR8148.