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The purpose of this study was to determine if Enterococcus spp. are more prevalent in endodontically treated teeth with periradicular lesions compared with teeth that require retreatment but have no periradicular rarefaction. Fifty-eight teeth that had received root canal therapy more than 1 yr previously and required retreatment were included. Designation of lesion versus no lesion was determined by two experienced endodontists. DNA extraction and PCR amplification were performed using ubiquitous 16S rDNA bacterial primers, as well as Enterococcus spp.-specific primers. The results showed that the overall prevalence of bacteria was 90% and Enterococcus spp. was 12%. χ2 analysis revealed a statistically significant relationship between the presence of a lesion and the presence of bacteria, as detected by the universal primers (p = 0.032). Using logistic regression, a statistically significant relationship was found between teeth with normal periapex and the presence of Enterococcus spp. (p = 0.023). This study revealed that bacteria are significantly associated with endodontic treatment failure but enterococci are not associated with disease.