The purpose was to compare the retention and caries preventive effect of Fuji VII and a resin-based sealant in children at high risk (HR) and low risk (LR) of caries. Fifty-seven schoolchildren (150 teeth) with completely erupted bilateral permanent first molars were included. The study was a split-mouth, randomized trial. Sealant retention and caries were evaluated after 6 months, 1 year and 2 years. After 2 years, there was no statistically significant difference in the incidence of caries between Fuji VII and Concise in the HR and LR groups. With Concise, LR children were less likely to have dental caries than HR. With Fuji VII, there was no difference in caries incidence between LR and HR. Retention of Concise was superior to that of Fuji VII. Our results suggest that Fuji VII and Concise sealants had similar caries preventive effects in children at high and low risk of caries.