BACKGROUND: Cost-effectiveness studies of lifestyle interventions in people at risk for lifestyle-related diseases, addressing 'real-world' implementation, are needed. This study examines the cost-effectiveness of a primary care intervention from a societal perspective, compared with provision of health brochures, alongside a randomized controlled trial. METHODS: Adults aged 30-50 years, at risk of type 2 diabetes (T2DM) and/or cardiovascular disease (CVD), were recruited from twelve general practices in The Netherlands. They were randomized to the intervention (n = 314) or control group (n = 308). The intervention consisted of up to six face-to-face counseling sessions with a trained practice nurse, followed by three-monthly sessions by phone. Costs were collected using three-monthly retrospective questionnaires. Quality of life was measured with the EuroQol-5D-3L, at baseline, 6, 12 and 24 months. Nine-year risk of developing T2DM and ten-year risk of CVD mortality were estimated using the ARIC and SCORE formulae, respectively, based on measurements at baseline and 24 months while applying a fixed age of 60 years at both time points. RESULTS: Small, statistically non-significant differences in effects were found between the intervention and control group with regard to risk scores and Quality Adjusted Life Years (QALYs) gained. The mean difference in costs between the intervention and control group was €-866 (95% confidence interval -2372; 370). The probability that the intervention was cost-effective varied from 93% at €8000/QALY to 88% at €80,000/QALY. CONCLUSION: A primary care lifestyle intervention aimed at adults at increased risk of T2DM and/or CVD could result in cost savings over a two-year period. However, due to methodological uncertainty no advice can be given regarding the implementation of the intervention in Dutch general practices. TRIAL REGISTRATION: Current Controlled Trials ISRCTN59358434.