Oestrogen plays major role in bone metabolism/remodelling. Despite of well-established effect of oestrogen deficiency on long bones, it remains unclear whether alveolar bone is affected. We aimed to determine the effect of oestrogen-deficiency in the alveolar bone microarchitecture. C57BL6/J and Balb/c mice were ovariectomized and implanted with oil-(OVX) or 17β-estradiol (E2)-containing (OVX + E2) capsules. Ovary-intact mice were used as controls. The dose of E2 replacement was selected based on trophic effects on the uterus and femur bone loss. As determined by maxillary alveolar bone MicroCT analysis, both C57BL6/J and Balb/c OVX mice displayed decreased trabecular thickness, bone density and bone volume, and increased trabecular separation at 15 and 30 days after ovariectomy. These effects were associated with a reduction of trabecular bone percentage and cortical thickness in the femur. A significant loss of alveolar bone crest was also associated with ovariectomy in both mice strains. The E2 replacement fully prevented ovariectomy-induced alterations in the alveolar and femoral bones. Moreover, TNF-α (tumour necrosis factor-α) levels and RANKL/OPG (receptor activator of NF-κB ligand/osteoprotegerin) ratio were increased in the maxilla after OVX, and these responses were also reversed by E2. In conclusion, oestrogen deficiency causes maxillary alveolar bone loss, which is similar to the effects found in the femur. The release of inflammatory molecules like TNF-α, RANKL and OPG is the potential mechanism to the decrease of bone quality and alveolar bone crest.