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To identify dominant microorganisms in root filled teeth with apical periodontitis by Pan-PCRs in comparison with a culture-dependent approach, focusing on fungal species profiling. The root filling material (gutta-percha) removed from 42 teeth with periapical radiolucencies undergoing root canal retreatments was analysed by molecular genetics techniques. Real-Time Pan-PCRs were conducted for the diagnosis of predominant bacteria (targeting 16S rDNA) and fungi (targeting ITS1-2 region). Identification of microorganisms was performed by