The aim of the present trial was to (1) compare the caries-preventive effect of glass ionomer sealants, placed according to the atraumatic restorative treatment (ART) procedure, with composite resin sealants over time and (2) investigate the caries-preventive effect after complete disappearance of sealant material. Forty-six boys and 57 girls, mean age 7.8 years, were randomly divided into two treatment groups in a parallel-group study design. A light-polymerized composite resin sealant material and a high-viscosity glass ionomer were each placed in 180 fully erupted first molars in their respective treatment groups. Evaluation took place annually for 5 years by calibrated examiners. After 5 years, 86% composite resin and 88% glass ionomer sealants did not survive. Three categories of re-exposure periods for caries development in pits and fissures after complete loss of sealants were distinguished: 0–1, 1–2 and 2–3 years. In the 2- to 3-year group, 13 and 3% of pits and fissures previously sealed with composite resin and glass ionomer, respectively, were diagnosed as having developed a dentine lesion. The relative risks (95% CI) of dentine lesion development in surfaces sealed with glass ionomer compared to those sealed with composite resin after 3, 4 and 5 years were 0.22 (0.06–0.82), 0.32 (0.14–0.73) and 0.28 (0.13–0.61), respectively. The relative risks of dentine lesion development in pits and fissures previously sealed with glass ionomer compared with composite resin over re-exposure periods of 1–2 and 2–3 years were 0.26 (0.14–0.48) and 0.25 (0.09–0.68), respectively. We conclude that the caries-preventive effect of high-viscosity glass ionomer sealants, placed using the ART procedure, was between 3.1 and 4.5 times higher than that of composite resin sealants after 3–5 years. Furthermore, high-viscosity (ART) glass ionomer sealants appear to have a four times higher chance of preventing caries development in re-exposed pits and fissures of occlusal surfaces in first molars than light-cured composite resin sealant material over a 1- to 3-year period. A well-designed clinical trial using different types of oral health personnel should be implemented to confirm these initial results.