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BACKGROUND/PURPOSE The aim was to assess the effectiveness of antimicrobial photodynamic therapy (aPDT) as an adjunct to mechanical instrumentation (MI) in reducing Enterococcus faecalis (E faecalis) and Candida albicans (C albicans) counts from C-shaped root-canals. METHODS Teeth with C-shaped canals as identified on cone beam computed tomographic images were included. Following incubation with E faecalis and C albicans, samples were divided into 4 groups a four follows: Group-1: MI with adjunct aPDT; Group-2: aPDT alone; Group-3: MI alone; and Group-4: no treatment. The pulp chambers of these teeth were exposed and coronal pulp was mechanically derided using sterile endodontic excavators. Using flexible files, all canals were debrided up to size #30 K-files with intermittent irrigation with 2.5% sodium hypochlorite irrigation. In Groups 1 and 3, methylene-blue was injected in all canals and aPDT was performed using a 600 nm diode laser. Sample-size estimation was done on data from a pilot investigation and group-comparisons were done using one way analysis of variance and Bonferroni post-hoc adjustment tests. P < .05 was considered statistically significant. RESULTS Sixty periodontally hopeless mandibular second molars with C-shaped canals were included. There was a statistically significant reduction CFU/mL of E faecalis (P < .001) and C albicans (P < .001). At post-operative microbial assessments in Group-1. There was no difference CFU/mL of E faecalis and C albicans at post-operative microbial assessments in Groups 2-4. CONCLUSION MI with adjunct aPDT is more effective in reducing count of E faecalis and C albicans from C-shaped root canals.