The aim of this trial was to compare the caries-preventive effect of sodium fluoride varnish and acidulated phosphate fluoride (APF) gel. A total of 254 children aged 12-13 years with high past caries experience were randomly divided into two groups. The participants received semi-annual applications of either fluoride varnish or APF gel for 3 years. During the study, the mean (+/- SD) total DMFS increments of the varnish and gel groups were 6.8+/-5.6 and 7.7+/-6.4, respectively, when initial caries was included, and 3.1+/-3.7 and 3.6+/-4.6 when initial caries was excluded. The difference was most evident on the approximal surfaces (varnish: 1.4+/-2.4; gel: 1.9+/-3.1). However, this difference was not statistically significant. Although larger studies are needed for firm conclusions about the comparative effect of the two fluoride measures, the results suggest that fluoride varnish is as effective as fluoride gel at least in preventing approximal caries. Taking into account the shorter treatment time, using fluoride varnish for professional applications seems justified.