Aims The purpose of this study was to clarify the histopathological reactions, growth and complications on immature rat molar with intraalveolar root fracture over 3–4weeks. Methods The upper first molars of 4-week old male Crlj:WI rats weighing 93.5–107.0 g were pushed horizontally toward the palate to cause a constant amount of dislocation by our previously developed experimental luxation model. The molars were then scanned using two types of 3-dimensional (3D) X-ray micro-computed tomography (μCT), and a 3D analysis was performed. Decalcified sections were also prepared and observed. Results In experimental group, root fracture occurred in four mesial roots out of eight teeth, and reparative dentin and cementum formed on the root fracture line over 3–4 weeks. On the periodontal side of the fracture, the surface of the dentin was covered with cementum, and partially covered with a large amount of cellular cementum. No distinct differences in root length were identified between the control group and the experimental group. All molars in the experimental group defined external root resorption. On the palatal area (cervical compression side), the depth and range of cervical external root resorption lacunae increased to 4 weeks. In experimental group, the width of periodontium tended to be larger than that in the control group, mesial tooth sockets had many blood vessels.