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Abstract Background Orthodontic debonding procedure produces inevitable enamel surface alterations, sequelae to which are enamel demineralization, sensitivity and retention of pigments. Several agents have been employed to counterbalance the same. The purpose of this study was (1) To evaluate the hypothesis that no significant difference exists in the remineralising potential of nano hydroxyapatite (NanoHAP) dentifrice and fluoridated dentifrice after orthodontic debonding, (2) To estimate the enamel topographic parameters following use of nano HAP dentifrice, post orthodontic debonding. Methods Sixty upper first bi-cuspids (30 subjects) planned for therapeutic extraction for the orthodontic treatment were bonded with a light cured adhesive. Envelope method of randomisation was followed in this prospective in-vivo study. In each subject, one of the first premolar brackets was debonded using a debonding plier and polished following standard protocols. Envelope method of randomisation was used to determine the side of the premolar to be debonded first. Patient was advised to use fluoridated (Group I) dentifrice for the first 15 days, then the first premolar was covered with a heavy-bodied putty cap, extracted and subjected to atomic force microscopy (AFM). Contralateral first premolar was then debonded and polished using similar protocol, and patient was advised to use nano hydroxyapatite dentifrice (Group II) for next 15 days. The premolar was then extracted and analyzed for surface roughness using AFM. The remineralizing potential of dentifrices was assessed by evaluating surface roughness parameters of the two groups and were compared using a two-sample t test. Results A significant difference was found amongst Group I (Fluoridated dentifrice) and Group II (NanoHAP dentifrice) (p > 0.001***) for enamel surface roughness variables which reflect remineralising potential of dentifrices. Group II showed significantly lesser value of surface roughness characteristics. Conclusions NanoHAP dentifrice was shown, after 15 days, to be superior to fluoridated dentifrice in remineralising enamel post orthodontic debonding.