Pit and fissure sealants have been considered an outstanding adjunct to oral health care preventive strategies in the decrease of occlusal caries onset and/or progression.Amorphous calcium phosphate (ACP) has been suggested to stimulate the repair of tooth structure through the release of cavity-fighting components including calcium and phosphate. Aim: to evaluate and compare the sealant retention rate, microleakage and quantitative energy dispersive x-ray analysis (SEM-EDX) of Calcium amorphous phosphate and Fluoride containing resin based pit and fissure sealants. Methods: Twenty five children from Ebad el Rahman orphanage at 6th October city were selected for this study. Fifty lower first permanent molars that were newly erupted, non carious and with plaque retentive fissures were selected in the study. All molars were sealed so that both types of fissure sealants were used in the same child (split mouth technique).They were equally divided into two groups. Group I: Resin based fissure sealant with Calcium amorphous phosphate. Group II: Resin based fissure sealant with Fluoride. Fissure sealant retention were evaluated after 3,6 and 9 months. The present study aimed also at evaluating the microleakage of Aegis (calcium amorphous phosphate resin based sealant.Moreover, this study evaluated the quantitative energy dispersive x-ray analysis (SEMEDX) for both types of fissure sealants at baseline, after 48h in carious solution after 2 weeks and 1 month in artificial saliva. Results: There was no statistically significant difference in the sealant retention rate between Group I and GroupII throughout the study period. There was no statistically significant difference in the median of microleakage score and percentage leakage between both groups. Group I had a borderline significant decrease in the mean ca/p ratio after 1 month in artificial saliva, however, Group II didn’t show any significant change up to 1 month of the study period..Although both groups showed decrease in the percent change of Ca/p level, these differences weren’t statistically significant. Conclusion: Satisfactory retention of both sealants was nearly the same by the end of the clinical study and both sealants had nearly similar microleakage scores. Fluoride containing fissure sealant showed better remineralization results than amorphous calcium phosphate containing sealant at the end of the study.