Background The clinical and economic burden of type 2 diabetes mellitus on society is rising. Effective and efficient preventive measures may stop the increasing prevalence, given that type 2 diabetes mellitus is mainly a lifestyle-driven disease. The Feel4Diabetes-study aimed to tackle unhealthy lifestyle (unhealthy diet, lack of physical activity, sedentary behaviour, and excess weight) of families with a child in the first grades of elementary school. These schools were located in regions with a relatively low socio-economic status in Belgium, Bulgaria, Finland, Greece, Hungary and Spain. Special attention was paid to families with a high risk of developing type 2 diabetes mellitus. Methods The aim of this paper is to describe the detailed methodology of the intervention's cost-effectiveness analysis. Based on the health economic evaluation of the Toybox-study, both a decision analytic part and a Markov model have been designed to assess the long-term (time horizon of 70 year with one-year cycles) intervention's value for money. Data sources used for the calculation of health state incidences, transition probabilities between health states, health state costs, and health state utilities are listed. Intervention-related costs were collected by questionnaires and diaries, and attributed to either all families or high risk families only. Conclusions The optimal use of limited resources is pivotal. The future results of the health economic evaluation of the Feel4Diabetes-study will contribute to the efficient use of those resources.