Miniscrews are being increasingly used for anchorage control in orthodontics. Despite the concern over root damage caused by miniscrews, there are few reports of precise clinical evaluations and appropriate management of that damage. In the case presented herein, the root damage caused by the placement of miniscrews was repaired by root canal treatment and surgical intervention.A 44-year-old man received orthodontic treatment for intrusion of the left maxillary first molar with a miniscrew anchorage system. During that treatment, the miniscrews had fallen out and had to be reinserted more than 6 times in the same area. Two years later, the patient complained of a spontaneous pain in the maxillary left molar region. Although the patient received root canal treatment, intraoral sinus tracts could still be detected, and the patient's discomfort persisted. Periradicular surgery revealed that the persistent infection was related to root surface damage caused by orthodontic miniscrew placement. Healing was achieved by a combination of root canal treatment and surgical intervention.Scanning electron microscopy of the damaged distobuccal root apex revealed a mature biofilm consisting of a network of matrix that contained mostly rod-like and spherical bacteria. At a 12-month recall checkup, the patient was free of pain. A repeat periapical radiograph revealed reduction of the pretreatment radiolucent lesion.More careful planning of miniscrew placement is necessary to lessen the danger of root damage. Furthermore, a precise evaluation of both root and pulpal damage and careful consideration of the choice of optimal treatment modality are needed.