The purpose of this study was to investigate if microleakage occurs in fissures after being sealed with a glass ionomer cement (Fuji III). Ten pairs of contralateral maxillary premolars, to be extracted for orthodontic reasons, were sealed in vivo. Glass ionomer cement was randomly used on one tooth and diluted composite on the contralateral. An air-polishing instrument was used for cleaning the fissures before sealing them. After 14 days the sealant status was recorded clinically and the teeth were extracted. They were placed in a 0.5% solution of methyl blue, subjected to a thermal cycling procedure, and finally sectioned. The sections were photographed in a stereomicroscope, and two observers recorded the microleakage according to a scoring system. Three glass ionomer sealings were clinically recorded as missing, one partly missing, and six intact, while all the resin sealings were present. Extensive leakage was seen in all glass ionomer specimens with dye penetration throughout the material as well as at the interface between cement and enamel. No leakage was seen in the composite specimens. Remnants of glass ionomer cement were observed in most of the sections from teeth which clinically seemed to have lost the sealing. This study indicates that Fuji III is poorly retained in the fissures, and that the material permits leakage even when it is fully retained. The material may, however, prevent caries by release of fluorides, and the fact that remnants of cement were found in fissures which clinically seemed to have lost it, indicates that this may even occur in cases with loss of retention.