Tooth agenesis is a common craniofacial congenital malformation in humans, but little is known about the mechanisms of root resorption in this condition. The purpose of this study was to investigate the mechanisms of root resorption in primary molars without successors. An animal model without permanent tooth germs was established by surgery in beagles. The times of onset of primary molar root resorption, with and without successors, were compared. The distribution of immune cells, odontoclasts, and their activating factors were determined by histochemistry and immunohistochemistry. Root resorption of primary mandibular molars without successors began later than physiological resorption. In primary molars without permanent germs, odontoclasts and immune cells were present mainly in the apical pulp at the start of root resorption, whereas in control teeth receptor activator of nuclear factor‐κB ligand (RANKL)‐positive cells were found mainly in the region of the periodontal ligament. CD14⁺ and CD3⁺ cells were found in both the pulp and the periodontal ligament region. These results suggest that the dental pulp of primary molars, as well as immune cells, may play an important role in root resorption in primary molars without permanent tooth germs.