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Background Glass ionomer sealants are an alternative to resin-based sealants, especially for use in partially erupted permanent molars. The authors conducted a study to compare the retention, marginal staining and cariostatic properties of a glass ionomer sealant with those of a resin-based sealant during a 24-month period. Methods We included in this study 39 patients aged 5 through 9 years who had bilateral partially erupted first permanent molars. One of us (S.B.) placed a resin-based sealant (Delton Plus FS+, Dentsply Professional, York, Pa.) (group D) on a partially erupted first molar in one quadrant of the maxilla or mandible and a glass ionomer sealant (GC Fuji Triage White, GC America, Alsip, Ill.) (group T) in the other quadrant. Two masked and calibrated investigators (S.A.A., J.C.) evaluated the sealants for retention, marginal staining and carious lesions at three, six, 12 and 24 months. The authors used a multinomial regression for statistical analysis ( P Results The recall rate was 69.2 percent at 24 months. Two sealants from group D and three from group T were lost completely. Complete retention rates at 24 months were 40.7 and 44.4 percent for groups D and T, respectively. The authors found no statistically significant difference in retention rates between groups at each recall examination ( P > .05). For marginal staining, sealants in the resin-based group exhibited statistically higher marginal staining than did sealants in the glass ionomer group ( P Conclusions Resin-based and glass ionomer sealants exhibited similar retention rates at 24 months. However, marginal staining was lower in the glass ionomer group, and the authors found no caries in teeth in this group. Consequently, glass ionomer sealants may be a better choice when salivary contamination is expected. Clinical Implications Sealing during tooth eruption presents a particular challenge owing to difficulty in isolating the tooth. Glass ionomers may be a better material for sealing partially erupted molars.