Endodontic infections include conditions such as pulp necrosis, apical periodontitis, abscesses, granulomas, and periapical cysts. Detection of pathogenic microorganisms responsible for these diseases is essential for accurate diagnosis and future therapy. Enterococcus faecalis, Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola were analyzed qualitatively and quantitatively using the Checkerboard methodology for DNA-DNA hybridizations as a bacterial identification tool. Clinical investigations have shown a significant frequency of these microorganisms. The present systematic review and meta-analysis aimed to determine the prevalence of E. faecalis and red complex bacteria (RCB) (P. gingivalis, T. forsythia, and T. denticola) analyzed by the Checkerboard DNA-DNA hybridization technique in endodontic infections. This systematic literature review followed the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines-electronic databases: PubMed, Scopus, ScienceDirect, Web of Science, and Google Scholar. Statistical analysis was performed using STATA V.15 software. Seventeen articles were included, of which a total of 620 samples were evaluated. Five hundred sixty-seven samples were taken from infected root canals, 34 samples from periradicular tissues, and 27 samples from periapical abscesses of infected teeth. The prevalence of E. faecalis in endodontic infections in all studies was 74 %, of P. gingivalis was 63 %, of T. forsythia 46 %, and of T. denticola 58 %. The presence of bacteria such as E. faecalis reduces the efficiency of endodontic therapy and leads to recurring infections. It is recognized that "RCB" can be identified in endodontic lesions
however, they are not usually prominent. The DNA-DNA hybridization approach is critical for identifying bacteria and detecting difficult-to-culture microorganisms, making it a helpful and cost-effective tool for directing personalized endodontic treatments.