A longitudinal case–control study was performed to measure the association of salivary biomarkers with alveolar bone loss from a sub-sample of 1,256 post-menopausal women enrolled in the Buffalo Women's Health Initiative. From this cohort, 40 subjects with significant alveolar bone loss over a 5-year period were compared to 40 age-matched control subjects having no alveolar bone loss. Several biomarkers were quantitated in saliva collected at baseline by immunoassay. A positive association was noted between alveolar bone loss and salivary concentrations of hepatocyte growth factor, and interleukin-1 beta, while a negative association was noted for alveolar bone loss and salivary osteonectin. This study provides preliminary evidence that several salivary biomarkers measured at baseline may serve to predict future alveolar bone loss.