Background: Tooth surface modification by root conditioning results in improved connective tissue attachment and advancement in the the goal of reconstructive periodontal treatment. Aim: Evaluation and comparison of novel root canal irrigant- MTAD and QMix on periodontally involved teeth. Settings and design: 30 teeth were collected and stored in saline. By making two parallel grooves with a cylindrical bur under copious saline irrigation, samples were taken from the cervical third of the root. First groove is prepared at cemento-enamel junction and another 7 mm apical to it. Root surfaces of the teeth were scaled with an ultrasonic scaler and thoroughly planed with #1-2, 3-4 Gracey curettes for the elimination of all the diseased cementum. The dentin sample of dimension 4 mm x 6 mm were prepared and stored in normal saline before use. Materials and method: Samples were randomly divided into three groups: BioPure MTAD ™, QMix TM 2 in 1 and saline. Specimens were actively burnished for 3 min and following treatment, were prepared for scanning electron microscopy and examined at 5000X magnification. Samples were scored according to sampaio’s index. Mann - Whitney U test and chi square tests were being applied. Results and conclusion: BioPure MTAD ™ is most efficacient in removing the smear layer and showed significant dentinal tubules opening followed by QMix TM 2 in 1 and saline.