The unequivocal role of microorganisms in the aetiology of apical periodontitis has been well established. As a consequence, successful treatment of this disease is contingent upon effective elimination or maximal reduction of the involved microbiota. There are at least two major aspects of endodontic infection that need to be well understood for establishing effective therapeutic protocols: the composition of the endodontic microbiota associated with the different forms of apical periodontitis and different types of infection (i.e. which are the main candidate pathogens); and the patterns of microbial colonisation within the root canal system (i.e. how they are distributed along the infected tissues). This review focuses on the current knowledge of these two aspects. Proper interpretation and clinical application of this information has the potential to be translated into improvements in quality and predictability of the treatment offered to patients. Keywords: apical periodontitis, endodontic infection, endodontic pathogens, root canal treatment