Background: This prospective multi-center (PURE) clinical study evaluated healing rates for molars after root canal treatment employing the GentleWave® System (Sonendo, Inc., Laguna Hills, CA). Material and Methods: Eighty-nine patients met the inclusion criteria and consented for this clinical study after referral for a root canal treatment. All enrolled patients were treated with the GentleWave System. Five endodontists performed the clinical procedures and follow-up evaluations. Pre-operative, intra-operative, and post-operative data were collected from the consented patients. Each patient was evaluated for clinical signs and symptoms. Two trained, blinded, and independent evaluators scored the subject tooth radiographs for apical periodontitis using the periapical index (PAI). The teeth classified as healing or healed were considered as a success and composed of a cumulative success rate of healing. Statistical analysis was performed by using the Fisher’s exact test, Pearson correlation, and multivariate logistic regression analyses of the pre-operative prognostic factors at 0.05 significance level. Results: Seventy-seven patients were evaluated at six months with a follow-up rate of 86.5%. The cumulative success rate of healing was 97.4%. Eleven prognostic factors were identified using bivariate analyses. Using logistic analyses, the two prognostic significant variables that were directly correlated to healing were the pre-operative presence of periapical index (p value=0.016), and single treatment visits (p value=0.024). Conclusions: In this six-month PURE clinical study, the cumulative success rate of healing was 97.4% when patients were treated with the GentleWave® System.