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Enterococcus faecalis is associated with a significant number of refractory endodontic infections. Previous studies report a prevalence of Ent. faecalis ranging from 24% up to 77% in teeth with failed endodontic treatment. The origin of the micro-organism remains unclear, as enterococci do not belong to the normal oral microflora. The aim of this study was to determine whether these enterococci were of endogenous or exogenous origin.Fifty consecutive patients with apical periodontitis in need of endodontic orthograde re-treatment were included. Samples were collected from root canals, saliva and faeces and subjected to microbiological culturing. The genetic relationship between Ent. faecalis from root canals and isolates from the different host sources was determined using pulsed-field gel electrophoresis. In 16% (8/50) of the patients, enterococci were collected from the root canal samples. The genetic analysis showed that the isolates from the root canals were not related to those from the normal gastrointestinal microflora. None of these patients had enterococci in their saliva samples.Endodontic infections with Ent. faecalis are probably not derived from the patient's own normal microflora, which indicates that these infections ent. faecalis are of exogenous origin.This is the first study to genetically compare endodontic infectious Ent. faecalis isolates with isolates from the hosts' own normal microflora.