This cluster randomised controlled study assessed the effectiveness of twice-yearly applications of fluoride varnish as a public health measure to reduce dental caries in children living in relatively deprived communities. The test (n = 334) and control (n = 330) children in 2 school years (unit of randomisation) attended 24 state primary schools and were 6–8 years of age at the start. Good baseline balance was found. Duraphat varnish was applied at school on 5 occasions over 26 months, by dental therapists. A combined visual and fibre-optic transillumination examination included all surfaces of primary and first permanent molars at baseline and after 26 months for small and large enamel and dentine lesions. At the final examination the only statistically significant difference was in the caries increment for small enamel lesions in the primary dentition, with the test children having fewer lesions. This study failed to demonstrate that the twice-yearly application of fluoride varnish provided at school reduced dental caries in children living in this community. The low level of response and a lower than expected caries increment had a major impact on the effectiveness of the intervention, since the children who participated were least likely to have benefited from the programme, whereas those who might have benefited did not consent.