Anatomic variations are common in human dentition. A clear understanding of these variations is very important for success of endodontic treatment. A dentist should be aware of these anatomic variations as this can affect the treatment outcome. A case of endodontic therapy is presented in which inability to locate an anatomically rare supplemental canal of a three rooted mandibular first molar resulted in treatment failure. A 21-year-old female reported with pain and swelling in relation to lower right first molar. An intra oral periapical radiograph revealed 3 roots; the first canal of the mesial root and a canal of one of the distal roots were found to be treated endodontically, which were infraobturated but the canal of the 2nd distal root had not been treated. The radiograph revealed periapical radiolucency and widening of periodontal space. Prior to starting the endodontic treatment the clinician must be aware of the anatomic variations in tooth pulp morphology and also the importance of preoperative radiographs cannot be underscored.