Abstract The objective of this study was to evaluate the clinical survival of sealants applied in first permanent molars (FPMs) affected by molar-incisor hypomineralization (MIH), at 18 months of follow-up. Forty-one first permanent molars were selected from 21 children, 6–8 years of age. MIH was classified by one calibrated examiner (kappa = 0.80) according to EAPD criteria. The inclusion criteria were fully erupted FPMs with MIH or sound FPMs (without MIH) for which sealant treatment was indicated. The FPMs were assigned to two groups: CG (control group) and HG (MIH group). Both groups were treated with sealant (FluroShield). Clinical follow-up was performed from baseline to 18 months to assess anatomical form, marginal adaptation, retention and presence of caries, according to criteria set by the United States Public Health Service-Modified, and was conducted by a blinded examiner (kappa = 0.80). The actuarial method was used to evaluate the survival of the sealants. The survival rates for the groups were compared using Fisher’s exact test (α = 5%). The cumulative survival rates were 81% at 1 month, 68.8% at 6 months, 68.8% at 12 months, and 62.6% at 18 months for CG, and 88% at 1 month, 84% at 6 months, 76% at 12 months, and 72% at 18 months for HG. No significant difference was found between the groups. The sealants in molars affected by MIH presented a survival rate similar to the sealants in the control, suggesting that sealants may be an adequate approach for preventing carious lesions in MIH-affected molars.