Objectives: To test the effectiveness of fluoride varnish in preventing caries in early childhood in children at high risk of caries. Basic research design: Randomized controlled trial. Participants: 504 participants, with mean age of 21 months at baseline randomly allocated into a test and a control group. 427 children remained in the study after two years. Intervention: Fluoride varnish applied four times a year, every three months. The intervention lasted for two years. Main outcome measures: Dental status was recorded based on the International Caries Detection and Assessment System (ICADS). Results: Mean dmfs was similar in the control and test groups at baseline (1.0 and 1.2 respectively) but was significantly different (10.1 and 5.2, p < 0.001, ANOVA) at endpoint. The proportion caries free in the two groups was 40% and 69.4% after two years. Conclusions: The application of fluoride varnish four times a year prevented the incidence and reduced the severity of caries in pre-school children. Trial registration number: DRKS00013980. Keywords: preschool children, early childhood caries, fluoride varnish, prevention