BackgroundBacterial infection plays an important role in persistent periapical lesions and inadequate disinfection of root canals is considered the biggest factor responsible for endodontic treatment failure. Antimicrobial Photodynamic Therapy (aPDT) has become the latest choice to eradicate microorganisms in root canals.ObjectiveThis study aims to evaluate the effectiveness of Antimicrobial Photodynamic Therapy (aPDT) in bacterial count reduction compared to Passive Ultrasonic Activation (PUI) and Ca(OH)2 dressings.Materials and methodsForty-five anterior single canal teeth with medium-sized periapical lesions (2–5 mm) were divided into three groups according to the disinfecting technique (each group consists of 15 canals with 1:1:1 allocation ratio): Group A: Ca(OH)2 dressing. Group B: Passive Ultrasonic Activation (PUI). Group C: Antimicrobial Photodynamic Therapy (aPDT). Direct bacterial viable count method was used to count the colonies forming units (CFU) before and after the disinfecting and the bacterial count reduction was estimated, the statistical analysis was performed at a 95% confidence level using the Chi-square and Mann–Whitney U test.ResultsaPDT showed no statistically significant difference when compared to passive ultrasonic irrigation (P > 0.05) but showed higher and more promising results when compared to Ca(OH)2 dressings (P < 0.05).ConclusionsaPDT has the ability and effectiveness as a disinfecting technique in necrotic and infected root canals.Clinical significance of the studyThe results of this clinical trial provide that aPDT can be considered an adjunct method for root canal disinfection with the same effectiveness as passive ultrasonic irrigation.