The aim of this study is comparing the retention and caries preventive effect of the glass-ionomer fissure sealant and resin-based fissure sealant. A randomized-controlled split-mouth study was conducted to compare the retention and the caries preventive effect of light-cured resin-based sealant (3M ESPE) and glass ionomer sealant (Fuji VII). The sealants were applied to either the right or the left lower mandibular molars (7-9 yrs of age) in 120 school children, based on the randomization process. They were recalled for assessment of clinical retention at intervals of 3, 6, and 12 months. The caries-preventive effect between the two materials was tested statistically by the McNemar's test for matched pairs, and the differences observed with regard to the retention of the materials was tested by Chi-square tests. The level of significance was set to be at P < 0.05. At the end of 12th month, sealant retention is found to be higher in the resin-based sealant group compared to the glass ionomer group. In the glass ionomer sealants placed, 101 (91%) were caries-free and 10 (9%) had caries. In the resin-based sealant, 105 (94.60%) had sound teeth and 6 (5.4%) had dental caries (P = 0.34). The glass ionomer sealant was less retentive when compared to resin sealants. The caries incidence between the glass ionomer and resin-based sealants was not statistically significant.