Aim: The present study was carried out to evaluate the relative efficacy of topical application of root conditioning agents such as citric acid, minocycline HCl solutions and EDTA gel preparation on periodontally diseased root surfaces. Material and methods: 60 specimens were obtained from the freshly extracted teeth and divided into4 groups, comprising of one control group and three experimental groups, each having 15 specimens. After scaling and root planing of teeth, these were resected first at level of cementoenamel junction and then longitudinally. Tooth was divided into 2 halves to obtain the dentin slabs of size 7x5 mm. These dentinal slabs were washed with and preserved in distilled water until the time of treatment. The particular solution or gel was passively applied to outer surface of dentin specimens with the help of cotton pellet saturated with that particular solution or gel preparation. These specimens were dehydrated in ascending order concentrations of aqueous alcohol solutions. Dried samples were mounted on SEM stubs. Specimens were then sputter coated with gold using sputtering device. The mounted specimens were evaluated using scanning electron microscope. The surface characteristics of root surfacewere evaluated descriptively, concerning the removal of smear layer, number of open dentinal tubules and the diameter of individual tubules, from the black and white camera prints. The data so obtained was compiled and subjected to statistical analysis. Results: Out of all the three root conditioning agents, the results of citric acid were better than minocycline HCl (highly significant) and EDTA (Non-significant). Conclusion: We concluded that root conditioning in all three experimental groups helped removal of smear layer, exposure of dentinal tubules and also the widening of dentinal tubules. Their application as root conditioner may have significant role in periodontal wound healing and future new attachment in-vivo.