Objectives: To analyze the ion exchange between conventional glass-ionomer restorative material, (Fuji IX-GC Co., Japan) and tooth components in primary molars after long periods of function in vivo. Methods: Five deciduous mandibular molars were collected after normal exfoliation. An intact deciduous molar served as control, a second deciduous molar was restored occlusaly with Fuji IX in vitro, and 3 deciduous molars with occlusal restorations were collected after 18, 24, and 48 months in vivo. The molars were sectioned bucco-lingual through the restoration and the chemical analysis was performed on enamel, dentin and restorative material along parallel lines crossing from buccal to lingual, using an energy dispersive X-ray spectrometer (EDS). The data was analyzed using SPSS program. Results: In the enamel adjacent to the glass-ionomer material, calcium and phosphate showed a significant reduction related to time (P<0.05). In both enamel and dentin strontium, silica and alumina migrated from the glass-ionomer material in significant concentrations (P<0.05), and fluorine showed an increase from zero in the intact deciduous molar to 1.2% after four years in vivo. In the glass-ionomer material fluorine was reduced in relation with time in vivo, while calcium concentration increased. Conclusions: There is a constant exchange of ions between glass-ionomer restorative material and tooth components in deciduous molars. It begins as early as two weeks in vitro and is increased in vivo. Strontium, alumina and fluorine released from the glassionomer have a bactericidal effect and may affect remineralization. Calcium may enhance the glass-ionomer mineralization and transform it into enamel like material. Clinical significance: The results showed that a continuous exchange of ions between enamel and dentin and glass-ionomer material occurs in vivo and the concentration of the ions is time related. Strontium, alumina and fluorine in enamel and dentin may cause a continuous anti bacterial and anti cariogenic effect, while calcium enhance mineralization of glass-ionomer in vivo, a factor that may increase the longevity of the restoration.