To evaluate the retention and caries experience effects of three different materials used as fissure sealants after 24 months of clinical application: a resin-modified glass ionomer cement (A), a flowable resin composite (B) and a compomer (C). One hundred and seventeen (117) teeth were sealed with material A, 119 teeth with material B and 120 teeth with material C. Children were randomly assigned. Each one received only one of the materials studied. Plaque index, dmft score and socioeconomic level were scored at baseline. The clinical exams were conducted 6, 12 and 24 months after application of the sealant. Statistical analysis (Kruskal-Wallis) revealed that there were statistically significant differences between the retention rates of groups A and B and between groups B and C after 2 years, with material B showing better results. After 2 years, 3.1% of the teeth of group A, 4.3% of group B and 6.7% of group C were Carious+Filled. There was no evidence of association between caries presence after 2 years and plaque index, dmft score and socioeconomic level. These results suggest that flowable resin composite had a satisfactory retention after this period of evaluation and all three materials were effective on occlusal caries prevention.