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The periapical abscess is a collection of pus in the pulp or around the root of teeth. Many odontogenic infections can be managed without antimicrobial therapy or bacteriologic investigation. However, when an acute bacterial infection has progressed or antimicrobial therapy might be of benefit to patients, antibiotics are prescribed. We aimed to identify microorganisms in root canals with periapical abscess and their antimicrobial susceptibility profile in order to revise antimicrobial treatment protocols when antimicrobials are used empirically.30 patients (all of whom had pain and swelling) with odontogenic infections were included in this study. The microbiologic investigation was performed under strict aseptic conditions. A standard routine root canal therapy was instituted, and in each case a single root canal was sampled. In multirooted teeth only the largest canal was sampled to preserve the identity of a single endodontic/microbiologic ecosystem. For microbial sampling, two sequential paper points were introduced into the full length of the canal, and kept in place for 1 min. One of the paper points was used for aerobic culture and the other one for anaerobic culture. To identify isolated bacteria, whole bacterial fatty acid profiles were evaluated by using a Microbial Identification System. Antimicrobial susceptibility results were obtained by disc diffusion test for aerobics, and E-test for anaerobics.In total, 156 bacterial strains were isolated. Eighty-six of them were aerobic and 70 of them were anaerobic. Eighteen (60%) cultured specimens were mixed (aerobic and anaerobic). The most prevalent bacteria were Staphylococcus spp. (aerobic), Peptostreptococcus prevotii and Streptococcus morbillorum (anaerobic).Beta-lactam antibiotics combined with beta-lactam inhibitor (amoxicillin-clavulanic acid) had a good effect on Gram (+) and Gram (−) aerobics. When we take into consideration that beta-lactam antibiotics stimulate production of beta-lactamase, amoxicillin-clavulanic acid combination appears a good first step antimicrobial therapy. Clindamycin may be a second alternative for that purpose. For anaerobics, cefoxitin and metronidazol had good effect. Although imipenem and piperasilin-tazobactam are perfect, they should not be the first step of therapy. Due to the frequency of mixed infections, a combination of amoxicillin-clavulanic acid and metronidazol or a combination of clindamycin and metronidazol have a good effect on mixed infections.