The aim of this study was to compare the caries prevention effectiveness, retention rates and the level of fluoride of saliva of a glass-ionomer sealant (GIS) with that of a resin-based sealant (RS). Eighty GIS and 80RS were placed on the first permanent molars in 40 children aged 7-10 years. Children were re-examined at 6, 12, 24, 36 and 48 months after the procedure. Saliva samples were collected before the sealant was applied and again at each appointment, and fluoride levels were measured. After 48 months, occlusal caries were seen in 4 and 12 teeth in GIS and RS groups respectively. There was a statistically significant difference in the fluoride levels of saliva between baseline and up to 12th month in GIS group. GISs presented effective prevention of caries development, even though the failure rate is higher when compared to the RSs. An increased salivary fluoride level due to GISs might be an additive effect on the prevention of dental caries.