A cost-effectiveness analysis was conducted during a 3-year randomized controlled clinical trial in a general dental practice in the Netherlands in which 230 6-year-old children (± 3 months) were assigned to either regular dental care, an increased professional fluoride application (IPFA) programme or a non-operative caries treatment and prevention (NOCTP) programme. Information on resource use during the 3-year period was documented by the dental nurse at every patient visit, such as treatment time, travel time and travel distance. Caries increment scores (at D₃MFS level) were used to assess effectiveness. Cost calculations were performed using bottom-up micro-costing. Incremental cost-effectiveness ratios (ICERs) were expressed as additional average costs per prevented DMFS. The ICERs compared with regular dental care from a health care system perspective and societal perspective were, respectively, EUR 269 and EUR 1,369 per prevented DMFS in the IPFA programme, and EUR 30 and EUR 100 in the NOCTP programme. The largest investments for the NOCTP group were made in the first year of the study; they decreased in the second and equalled the costs of control group in third year of the study. From both medical and economic points of view, the NOCTP strategy may be considered the preferred strategy for caries prevention.