It is generally accepted that a major cause of the failure of root canal therapy is an inability to localize and treat all of the canals of the root canal system. The risk of missing anatomy during root canal treatment is high because of the complexity of the root canal system. All categories of teeth may have extra roots and/or canals, but the likelihood of finding aberrant canal configurations is higher in premolars and molars. In addition, lateral ramifications of the root canal system may be present in all teeth with a significant frequency, increasing the probability of leaving untreated spaces after root canal therapy. Prevention of missed anatomy starts with good pre-operative radiographs, even though radiographs have limitations in assessing the number of canals and the presence of accessory canals and anastomoses. A correct access cavity preparation is of central importance in localizing the orifices of the root canals. However, to find hidden canals, an adequate armamentarium is required; the dental operating microscope and/or high-power loupes, used in conjunction with a headlight system, will provide enhanced lighting and visibility, whereas ultrasonic tips and long shank round burs with small shaft diameters will allow a controlled and delicate removal of calcifications and other interferences to the canal orifices. The impact of missed anatomy on the outcome of endodontic treatment is difficult to assess, and the literature on this subject is limited; a promising approach for future investigation may be a comparison of the number of canals found in failed treatment cases and after re-treatment. The clinical impact of missed anatomy can be clearly demonstrated with a large number of re-treatment case reports available in the literature; in the majority of these cases, failure of endodontic therapy is associated with untreated canal space. Localization and treatment of this missed anatomy typically leads to complete clinical and radiographic healing.