A double-rooted maxillary incisor is an extremely rare anatomic variation. Only a few case reports describe this abnormal anatomy. In recent decades, cone-beam computed tomographic (CBCT) imaging has become more common for endodontic purposes. This case report describes the retreatment of double-rooted maxillary central incisors using CBCT imaging. In 2012, a 20-year-old man was referred to our department because of asymptomatic periapical lesions in teeth #8, #9, and #10. During the evaluation of a periapical radiograph, a rare anatomic variation, in the form of an additional root of tooth #9, was detected, and it was impossible to decide about the source of the lesion between teeth #9 and #10. During retreatment, after gutta-percha removal, CBCT imaging was performed; this allowed proper treatment of the additional root and a final diagnosis of normal periapical tissue of tooth #10 with no treatment needed. The 18-month follow-up revealed a healing lesion in tooth #9 and normal periapical tissue in tooth #10. During the treatment of teeth with an anatomic variation, CBCT imaging can serve as an auxiliary tool for 3-dimensional evaluation that influences treatment steps and techniques. CBCT scanning can be very useful in assessing the actual location of a periapical lesion, which influences diagnosis and treatment planning.