OBJECTIVE The purpose of this study was to report the application of antimicrobial photodynamic therapy (aPDT) via sinus tract associated with laser phototherapy (LPT) in conservative treatment of a late failure of endodontic retreatment in two clinical cases of post-treatment apical periodontitis. BACKGROUND DATA Post-treatment apical periodontitis is a microbiological matter, because infection is present in almost all cases associated with this condition, even in teeth with apparently adequate root canal treatments. Infection is usually located within the root canal system, but in a few cases it may spread to the periradicular tissues. Many biofilms are susceptible to aPDT, particularly in dental disease. In the present two cases reports, aPDT was applied via sinus tract. METHODS In the two clinical cases, endodontic retreatment was unsuccessful, with the presence of a persistent swelling sinus tract, despite the standard quality of the endodontic retreatment. Before any surgical intervention, a noninvasive aPDT via sinus tract was performed. The photosensitizer methylene blue (0.01%) was inserted through the entrance of the sinus tract. Laser irradiation was performed perpendicularly (660 nm, 40 mW, 90 J/cm(2), 63 sec/point) directly over the entrance of the sinus tract. LPT (808 nm, 100 mW, 210 J/cm(2), 59 sec/ point) was applied after each aPDT session. Seven (case 1) and 10 (case 2) successive aPDT applications were performed followed by LPT. RESULTS The 18 month follow-up after treatment revealed control of the swelling sinus tract and diminishing of persistent apical periodontitis. The treatment succeeded, avoiding both surgical interventions and antimicrobial prescription. CONCLUSIONS The protocol of aPDT associated with LPT applied via sinus tract was revealed to be efficient for clinical infection control, and was found to be safe and conservative.