Especially in molars that may have sometimes aberrant additional root canals, the complexity of tooth internal morphology in individual cases sometimes does not match to admitted classification rules and underlines the risk of missed anatomy during the endodontic management. To our knowledge, a permanent mandibular second molar with independent five roots, three mesial and two distal, each of them harboring a single canal, was not yet reported. Despite the treatment difficulties this tooth could be successfully approached by using dental operative microscope and cone-beam computed tomography (CBCT) with small field of view. Though CBCT is not a routine imagistic examination, in case of atypical tooth anatomy aiming to establish adequate diagnosis and treatment plan, the successful clinical outcome prevails over the irradiation dose.