Objective: This manuscript shows if enamel deproteinization along with an intermediate layer of bonding enhances the retention of pit and fissure sealants.. Study Design: Two hundred six mandibular first permanent molars were allocated to Group I (n=103) and Group II (n=103). Group I underwent deproteinization, acid etching, bonding agent application and pit & fissure sealant placement while Group II treated with acid etching followed by pit & fissure sealant application only. Clinical analysis of all the teeth in the two groups was performed at 1, 3, 6, 9 and 12 months respectively. Pearson's chi – square test was utilized to evaluate the success of both treatment procedures (p<0.05). Results: At 12 months follow up the differences between the groups pertaining to Marginal integrity, Marginal discoloration and Anatomical form were statistically significant suggesting enhanced retention in Group I. Conclusions: Enamel deproteinization along with the use of intermediate bonding layer significantly enhances the retention of pit and fissure sealants in terms of enhanced marginal integrity, decreased marginal discoloration and preserving the anatomical form.