Although numerous studies have been conducted on apexification using mineral trioxide aggregate (MTA), direct observation of extracted human teeth after the procedure has been rarely reported. This case report describes a mandibular premolar treated 2.5 years ago and extracted recently for orthodontic treatment. The tubercle of the right mandibular premolar of a 12-year-old boy with dens evaginatus was fractured and the pulp was exposed. The tooth was diagnosed with pulp necrosis and asymptomatic periapical abscess. During the first visit, copious irrigation was performed with 2.5% sodium hypochlorite. Calcium hydroxide paste was placed as an intracanal medicament. The sinus tract had disappeared at the second visit after 3 weeks. MTA was applied on to the bleeding point as a 4-mm-thick layer, followed by a 3-mm-thick gutta-percha filling and resin core build-up. After 2.5 years, the tooth and three other premolars were extracted for orthodontic treatment. The right and left mandibular premolars were scanned with micro-computed tomography to determine the root shape and canal anatomy. Irregular root growth was observed and the root outline of the right mandibular premolar differed from that of the contralateral tooth. Apexification with MTA leads to the formation of roots with irregular morphology, without any pulpal space.