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Next‐generation sequencing (NGS) has now been applied for a decade to characterize the microbiota composition of infected dental root canals associated with apical periodontitis. Here, the study aims at systematically and critically reviewing these reports within the outcome of interest selected; the microbiota composition in different endodontic infection types. Standard methodological guidelines as stated by the PRISMA and the Joanna Briggs Institute are followed, including a risk of bias assessment. A literature search is conducted using the PubMed Advanced‐Search Builder on April 8, 2019; only original research articles that investigated the microbiota of infected root‐canals by means of NGS are screened. Among the 26 articles initially identified, 18 are included and evaluated for the following parameters; sampling protocol, sequencing strategy, and microbiota composition. The endodontic infections …