Objective The objective of this study was to compare the effect on periodontal health of ultrasonic versus manual scaling of the lower second molar (L2M) root surface following surgical extraction of mesioangular lower third molars (L3M). Study design Randomized single-blind clinical trial to compare the effectiveness of ultrasonic scaling of the L2M (experimental group) and manual scaling and root planing (control group) after surgical extraction of the corresponding L3M. Results Forty-three subjects were enrolled, 69.8% completing the study. The postoperative bony defect on the distal surface of the L2M was significantly reduced for both treatment groups ( P = .001). Despite a higher reduction of intrabony defect being observed in the ultrasonic group, the difference was not significant ( P = .17) at 6 months. Furthermore, there was also no statistically significant correlation ( P > .05) between the postoperative pocket depth and the treatment group (ultrasonic or manual). Conclusions Pocket depth and depth of the intrabony defect were similar in both experimental and control groups.