Objective To compare the retention and caries prevention of fissure sealant on the primary molars etched with self-etching adhesive and phosphoric acid in children. Methods 43 children younger than 42 months with more than 4 decayed teeth were studied. The split-mouth design was used in this study. The second and/or first primary molars were randomly assigned into self-etching adhesive group in one side of mouth, and phosphoric acid group in the other side. Sealants were applied on 69 pair primary molars according to manufacturer′ s instruction with dental cotton-roll isolation. The children were followed up every 3 months, and the sealants were observed and evaluated. In the case caries occurred, the teeth were restored. Results After 3 months, the retention rate was 93% in self-etching adhesive group and 100% in phosphoric acid group. At 6, 12 and 18 months, the retention rate of self-etching adhesive group was statistically lower than that of phosphoric acid group(P