OBJECTIVES:: Health economic objective to establish the cost of Fissure Sealants (FS) and Fluoride Varnish (FV) delivered in a community/school setting and the relative cost-effectiveness of these technologies. METHODS:: A randomised controlled allocation-blinded clinical trial. 1016 children aged 6-7 years were randomised to receive either FS or FV. Costs of the interventions; health care utilisation costs associated with travel or caregiving/time of work for families; costs associated with the schools e.g. as a result of child absence. The CHU-9D was used to generate utility values for each health state to enable the calculation of QALYs. RESULTS:: The intervention costs of the two technologies were £74.12 for FS and £64.16 per child over the course of the trial. The costs of the two technologies showed small but statistically significant differences between arms; for NHS (including intervention costs), the costs of FS versus. FV was (£500 versus. £491) with a mean difference of £68.13 (95% CI 5.63-130.63, p= 0.033) compared to FS. Results remained consistent across all scenarios used in the health economic analysis i.e. FV was less costly compared to FS. The CEAC showed that there was a 70% probability of FV being cost-effective within a societal WTP threshold of £20,000 per QALY. CONCLUSIONS:: In a community oral health programme utilising mobile dental clinics and targeted at children with high caries risk, twice yearly application of fluoride varnish resulted in caries prevention which is not significantly different from that obtained by applying and maintaining fissure sealants after 36 months. Fluoride varnish proved less expensive than fissure sealant. More work is needed on the use of the QALY and QATY in dental health research. The cost per QATY analysis undertaken in this trial allows the consideration of a dental health state utility. The effectiveness of the FS and FV following cessation of active intervention merits investigation.