Root debridement by scaling and root planing may not completely remove contaminated cementum particularly in more apical areas. The smear layer formed during root planing inhibits cell migration and attachment leading to impaired marginal periodontal healing. The present study was done to compare the morphological effects of root surface demineralization using citric acid and EDTA as root-conditioning agents. Thirty fragments of human dental roots previously exposed to periodontal disease were scaled and randomly divided into the following groups of treatment: Group I: Hand instrumentation and conditioning with normal saline for 5 minutes as control; group II: Hand instrumentation and conditioning with citric acid (pH 1) for 5 minutes and group III: Hand instrumentation and conditioning with EDTA (pH-7.4) for 5 minutes. Scanning electron microscopy was used to check for the presence of residual smear layer and for measuring the number and area of exposed dentin tubules. The mean efficacy of smear layer removal was compared between groups I and II, groups I and III and groups II and III, it was found to be statistically significant at 5%. When the mean diameter of the dentinal tubules and mean total surface area occupied by the dentinal tubule orifices was compared between groups II and III it was found to be statistically significant at 1% level of significance. Citric acid causes greater degree of morphological alterations than EDTA and is considered to be a better root-conditioning agent. However, the use of EDTA cannot be ruled out. This study supports the hypothesis that demineralizing agents can be used as an adjunct to the periodontal treatment aiming at restoring the biocompatibility of roots and helps in choosing an appropriate agent for root conditioning.