OBJECTIVE To investigate the factors associated with the change in alveolar bone level of mandibular second and third molars after second molar protraction into the space of the missing first molar (L6) or second premolar (LE). METHODS Fifty-one patients in whom space of the missing L6 or LE was treated with second molar protraction (13 males, 38 females, mean age 19.6 ± 4.7 years) from 2003 to 2015 were included. The alveolar bone level and position and angulation of the mandibular second and third molars were measured in panoramic radiographs at pre-treatment (T1), and after the alignment of the third molars following second molar protraction (T2). Factors associated with alveolar bone loss on the distal aspect of the mandibular second molars were assessed using linear regression analysis. RESULTS Age at T1 (P < 0.001) and third molar angulation at T1 (P = 0.002) were significant factors for the prediction of alveolar bone level distal to the second molars. CONCLUSIONS This study used two-dimensional panoramic radiographs, and we could observe only the interproximal bone level. CONCLUSIONS After second molar protraction into the missing first molar or second premolar space, mandibular second molars may exhibit alveolar bone resorption in the distal root in older patients and in those with mesially tilted third molars before treatment.