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The presence of the microorganisms of untreated canals is one of the main reasons of the failure in the endodontic treatment. The knowledge of variations in the canal systems of the tooth is important for the successful endodontic treatment. In the maxillary molars, the presence of the two separate palatal roots is very rare variations. Although there have been several case reports of maxillary first and second molars, the case reports of maxillary third molars are very few. This case report presents the endodontic treatment of a maxillary third molar with two separate palatal roots. It is important to notice the clinical signs and analyze the radiographs carefully. The use of a microscope is helpful for the visualization of pulpal chamber, and pulpal chamber floor should be investigated thoroughly with endodontic explorer. The straight-line access for all the canal orifices is important for the success in the endodontic treatment.