Studies of the microbiota from the canals of teeth with failure of endodontic therapy have revealed that it differs markedly from that of untreated necrotic dental pulps. This study aimed to evaluate the microbiota of 30 root-filled teeth with persisting periapical lesions and to test the antibiotic susceptibility of the most prevalent species. Microbial samples, isolation and speciation were done using advanced microbiologic techniques for anaerobic species. A total of 55 bacterial species were isolated, 80% were gram-positives and 58% facultative anaerobic microorganisms. The bacterial genera most frequently recovered were Enterococcus, Streptococcus, Peptostreptococcus and Actinomyces. Antibiotic sensitivity of Enterococcus faecalis and Peptostreptococcus spp. was accomplished with the E-test system. All species studied were susceptible to benzylpenicillin, amoxicillin, amoxicillin combined with clavulanate. However, 20% of the E.faecalis strains were resistant to erythromycin and 60% to azithromycin. It was concluded that microbial flora in canals after endodontic failure comprised predominantly facultative anaerobes and gram-positive species. E.faecalis was the species most frequently isolated and showed erythromycin and azithromycin resistance among the isolates.