The endodontic treatment of immature permanent teeth with necrotic pulp is a significant clinical challenge. The success of regenerative endodontic procedure is highly dependent on disinfection of the root canal and an accurate anatomical knowledge of the root canal. The aim of this study was to use micro-computed tomography (micro-CT) analysis to investigate the configuration of root canals in the upper permanent third maxillary molars with incomplete root development in their coronal, apical and middle third portions. Thirty immature third permanent maxillary molars were scanned using a micro-CT system. Then, we measured the diameters and areas of the root canal in the coronal, middle and apical third of the roots. The ratio between the long and short diameter of each root canal was then calculated and the canals were divided into several groups: round, oval, long oval, flat and irregular. The round configuration was not observed in the distobuccal and mesiobuccal roots in any of their anatomical regions. Oval and long oval canals predominated in the distobuccal root. The greatest variations were observed in the mesiobuccal root, with the ribbon-shaped canal predominating in the middle region and an irregular shape in the apical region. In the coronal region of the palatal canal, the round configuration predominated; in the middle third, we observed an almost equivalent distribution between round and oval configurations; apically, the oval shape predominated. In conclusion, we observed significant complexity and variation in the morphology and configuration of root canals in immature permanent molars, thus generating additional obstacles for the success of regenerative endodontics.