The aim of this case report is to describe a rare case of a five-rooted maxillary second molar that had two separated buccal roots and three separated palatal roots, each containing one independent root canal. The case report demonstrates that anatomical variations in the maxillary second molar should be taken into consideration during endodontic treatment, coupled with application of advanced techniques such as endodontic microscopy and cone-beam computed tomography to increase the ability of clinicians to treat difficult cases. Keywords: anatomical variations, cone-beam computed tomography, maxillary second molar, root canal anatomy, root canal therapy