In this narrative review, the potential reasons for the high occurrence of enterococci in filled root canals are explored. The pulpless root canal appears to be a habitat for these bacteria, particularly for Enterococcus faecalis. However, re-surveying the literature in caries research, it can be concluded that, contrary to earlier belief, enterococci are rare if ever found at the advancing front of dentinal lesions. The same is the case for true primary endodontic infections, but some uncertainty remains, because the coronal seal and the history of teeth harbouring enterococci have rarely been accurately investigated. Furthermore, from longitudinal studies with a known infection at the initiation of treatment, which was carried out under controlled asepsis, it is questionable whether enterococci are as difficult to eliminate from the canal system as is commonly held. A more likely explanation for the high occurrence of enterococci in filled root canals is that they enter after treatment, but from which source? The intriguing finding in this context is that enterococci do not appear to be colonizers of the oral cavity. They are merely transient oral bacteria, unless there is a predilection site such as the unsealed necrotic or filled root canal. The origin of this infection is most likely food. Using the example of enterococci in filled root canals, this paper highlights the possible importance of transient microorganisms in the oral cavity and changes in a microenvironment that can create favourable conditions for infection.