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The ability to properly shape and debride root canals has been made a good deal easier with the advent of rotary driven Ni-Ti files. The problem remains that due to the inherently complex internal architecture of the root canal system it has been problematic to ensure adequate removal of pulpal remnants and any associated biofilm. Research shows it takes 30 minutes immersion in dilute hypochlorite to disinfect the interior of a root canal to the depth of 0.5mm. Bacteria can colonise the interior of the root canal to the depth of 1mm or more and by communication through periodontal pockets and lateral canals a biotica can be present in areas not amenable to conventional instrumentation and disinfection. Root canals have complex systems of side tributaries radiating from the principal root canal and when we try and irrigate the apical area there may be air and fluid entrapment. Irrigants are not likely to properly wash out the apex and forceful irrigation can be associated with fluids being expressed through the apex with potentially serious adverse consequences. It is also a problem that some of the pathogenic bacteria are pretty tough to destroy: Enterococcus faecalis for instance is multi antibiotic resistant and can form a viable spore in the presence of hypochlorite or calcium hydroxide. Infected root canals often have had bacterial colonies that have been subject to several courses of antibiotics and this can result in resistance to further antibiotic chemotherapy. In view of these many problems it is not surprising apical radiolucency is a frequent asymptomatic finding on periapical radiographs.