Microorganisms play a critical role in the etiology and pathogenesis of apical periodontitis. Enterococcus faecalis and Candida sp. are frequently associated with persistent infections. The aim of this study was evaluated the antimicrobial photodynamic therapy (aPDT) as an adjunct of the endodontic treatment. Ten uniradicular teeth [control group (CG)=4 and test group (TG)=6] with primary endodontic infections were analyzed. Microbiological samples were collected before and after the chemical-mechanical instrumentation (CMI), after the aPDT (for the TG) and after the temporary restorations removal (second session).