BackgroundThe purpose of this study was to analyze the bacterial diversity in persistent apical lesions on root-filled teeth by using culture-independent molecular methods.DesignTwenty surgically removed apical lesions from therapy-resistant teeth were examined for the presence of bacterial DNA using PCR targeting the 16s ribosomal RNA gene, followed by cloning and sequencing.ResultsBacterial DNA was detected in 17 of the 20 samples (85%). A total of 236 clones were analyzed. Seven different bacterial phyla were represented and a total of 75 different bacterial taxa were identified; 36% of the species have not yet been cultivated. Commonly detected bacterial species included Fusobacterium spp., Prevotella spp., Tannerella forsythia, Porphyromonas endodontalis, Treponema denticola, Bacteroidetes spp., Peptostreptococcus spp., and Streptococcus spp.ConclusionsA wide range of bacteria was identified in periapical lesions on therapy-resistant teeth. These bacteria may contribute in the etiology of periapical infection and impede healing of these lesions.