Although there is some consensus that carious lesions in early stages (non-cavitated) could be treated using sealants, neither the type of materials nor their use in lesions with localized enamel breakdown (microcavitated) has been reported To compare the efficacy of resin or glass ionomer (GI) sealants in arresting microcavitated carious lesions (ICDAS 3) in first permanent molars.A double-blinded randomized controlled clinical trial was conducted in 41 healthy 6 to 11-year-old children. At the baseline examination, each subject had at least one carious lesion classified as ICDAS 3 on the first permanent molar. One hundred fifty-one lesions were randomized into: Group 1: resin sealants (76 lesions) and Group 2: GI sealant (75 lesions). Carious lesion progression was assessed clinically and radiographically. Progression and retention failure were the outcomes used for group comparisons at p-value<0.05.After a two-year follow-up, only one lesion progressed to ICDAS 5, without statistically significant differences between the groups (χ(1) = 0.90, p = 0.53). Radiographically, 100 lesions (98%) were arrested and 2 (2%) showed radiographic progression, without differences between groups (χ(1) = 0.93, p = 0.93). At 2 years, complete retention was observed in 77% of the resin-based and in 83% of the GI sealants, without statistical differences between type of sealant (χ(1) = 0.71, p = 0.48). The multilevel mixed model demonstrated that location and type of sealant did not affect retention rates (χ(1) = 24,98, p < 0.001).Sealing ICDAS 3 carious lesions in permanent molars appears to be effective in arresting lesions after a two-year follow-up. Clinicaltrials.gov: RCTICDAS3/2015.Minimally invasive approaches for carious lesion management have been promoted. Using sealants for the treatment of microcavitated lesions (ICDAS 3) appears predictable in the routine practice, without predilection for resin or glass ionomer materials. In addition to preserving tooth structure, this strategy reduces chair-time, dental fear and costs, and increases coverage to dental care.