Bacterial sampling of prepared root canals is used to determine the presence and character of the remaining microbiota. However, it is likely that current sampling techniques only identify organisms in the main branches of the root canal system whereas it is unlikely that they can sample areas beyond the apical end-point of preparation and filling, or in lateral canals, canal extensions, apical ramifications, isthmuses and within dentinal tubules. Thus, it may be impossible by current techniques to identify residual post-treatment root canal infection. In histologic observations of root apices, bacteria have been found in inaccessible inter-canal isthmuses and accessory canals often in the form of biofilms. There is no in vivo evidence to support the assumption that these bacteria can be entombed effectively in the canal system by the root filling and thus be rendered harmless. As a consequence of this residual root infection, post-treatment apical periodontitis, which may be radiographically undetectable, may persist or develop as a defence mechanism to prevent the systemic spread of bacteria and/or their byproducts to other sites of the body. Histologic observation of root apices with surrounding bone removed from either patients or human cadavers has demonstrated that post-treatment apical periodontitis is associated with 50–90% of root filled human teeth. Thus, if the objective of root canal treatment is to eliminate apical periodontitis at a histological level, current treatment procedures are inadequate. It is essential that our knowledge of the local and systemic consequences of both residual post-treatment root infection and post-treatment apical periodontitis be improved. The continued development of treatments that can effectively eliminate root infection is therefore a priority in clinical endodontic research. Post-treatment disease following root canal treatment is most often associated with poor quality procedures that do not remove intra-canal infection; this scenario can be corrected via a nonsurgical approach. However, infection remaining in the inaccessible apical areas, extraradicular infection including apically extruded dentine debris with bacteria present in dentinal tubules, true radicular cysts, and foreign body reactions require a surgical intervention.