Purpose: This study introduces a standardized 2-plane approach using 8 landmarks to assess alveolar bone levels in mice using micro-computed tomography. Materials and Methods: Bone level differences were described as distance from the cemento-enamel junction (CEJ) to alveolar bone crest (ABC) and as percentages of vertical bone height and vertical bone loss, comparing mice infected with Porphyromonas gingivalis (Pg) to controls. Eight measurements were obtained per tooth: 2 in the sagittal plane (mesial and distal) and 6 in the coronal plane (mesiobuccal, middle-buccal, distobuccal, mesiolingual, middle-lingual, and distolingual). Results: Significant differences the CEJ-to-ABC distance between Pg-infected mice and controls were found in the coronal plane (middle-lingual, mesiobuccal, and distolingual for the first molar; and mesiobuccal, middle-buccal, and distolingual for the second molar). In the sagittal plane, the distal measurement of the second molar was different. The middle-buccal, mesiobuccal, and distolingual sites of the first and second molars showed vertical bone loss relative to controls; the second molar middle-lingual site was also different. In the sagittal plane, the mesial sites of the first and second molars and the distal site of the second molar showed loss. Significantly different vertical bone height percentages were found for the mesial and distal sites of the second molar (sagittal plane) and the middle-lingual and distolingual sites of the first molar(coronal plane). Conclusion A reliable, standardized technique for linear periodontal assessments in mice is described. Alveolar bone loss occurred mostly on the lingual surface of the coronal plane, which is often omitted in studies.