Abstract
BACKGROUND: Effective disinfection is a diligent step in the treatment of endodontic infections to reduce the microbial load below a critical level that promotes healing of apical periodontitis (AP). Despite its clinical importance, there is no consensus on the most effective disinfection strategy to achieve this goal. Therefore, this scoping review aimed to comprehensively review the role of current disinfection therapies in microbial reduction during root canal treatment (RCT). METHODS: A systematic search was conducted in PubMed, Web of Science, Scopus, and Google Scholar. Relevant clinical studies were selected based on predefined inclusion criteria. Data extraction focused on microbial load reduction, disinfection protocols, and microbial detection techniques. RESULTS: Out of 3519 retrieved articles, 148 were eligible and processed for data extraction. All included studies were clinical studies. Most of the studies were primary RCT (82.43%) and secondary RCT (15.54%). While only 3 studies (2.03%) included both primary and secondary RCT. Microbial load reduction was assessed in the majority of the studies, while few others assessed endotoxin reduction. The mean percentage of microbial load reduction was (87.24 ± 21.86). The most frequently used disinfection regimens were irrigation with; (2.5% NaOCl alone, 2.5% NaOCl followed by 17% EDTA, 2%CHX; 16.05%, 11.11%, 10.49% respectively), activation methods including; passive ultrasonic irrigation (PUI); 12.35%, photodynamic therapy (PDT); 11.11%, and laser; 11.11%) and intracanal medication (ICM) with Ca (OH)2, Ca (OH)2 + 2%CHX, or 2%CHX; 31.48%, 10.51%, 7.41% respectively. The most prevalent methods of microbial detection were culture-based (64.86%), and molecular-based methods were performed in 58.10% of the studies. CONCLUSION: A combination of advanced irrigation techniques, appropriate ICM, and adjunctive disinfection activation techniques provides the most effective approach for both microbial and endotoxin reduction. However, complete disinfection and its influence on the validity of treatment outcomes remain a dilemma. The healing of apical periodontitis is multifactorial, and future research should focus on personalized treatment protocols based on patient and tooth specific considerations to optimize clinical outcomes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12903-026-07952-0.