Periodontal disease induces an increased incidence of tooth loss, particularly in cases with an associated loss of alveolar bone and periodontal ligaments. In this study, alveolar bone loss was detected by micro-computed tomography (CT) following exposure to E. coli lipopolysaccharide (LPS) in a streptozotocin (STZ)-induced diabetic mouse model. A 10 mg/ml dosage of E. coli LPS was applied between the first, second and third molars of the mice three times a week for 10 weeks. The loss of periodontal ligaments and alveolar processes was then evaluated by micro-CT using two and three dimensional microstructure morphometric parameters. In the diabetic mice, E. coli LPS induced the destruction of periodontal ligaments and loss of alveolar process spaces. The distances between periodontal ligaments were significantly widened in the STZ-LPS group compared with the untreated STZ group. The 10 mg/ml exposure to E. coli LPS in the STZ mice also resulted in a significant decrease in the alveolar bone volume fraction. The results of our study suggest that alveolar bone loss can be readily detected by volumetric micro-CT analysis as an increase in the distance between periodontal ligaments and in the alveolar process length.