Objective: To investigate the correlation between benign paroxysmal positional vertigo (BPPV) and abnormal bone metabolism and to evaluate the value of otoconial protein otoconin-90 in the pathogenesis research and clinical treatment of BPPV. Study Design: Prospective pilot clinical trial (Level of Evidence: 2b). Setting: Outpatient otolaryngologic department. Patients: Twenty seven patients with a diagnosis of BPPV referred to the otolaryngologic department and 25 controls with no history of dizziness from 2018.4 to 2018.9 were reviewed. Interventions: No. Main Outcome Measures: Dual-energy x-ray absorptiometry scanning (DEXA), bone mineral density (BMD) measurement, and assessment of serum levels of otoconin-90 and bone metabolism indices (osteocalcin, OC; 25-OH Vitamin D; total procollagen type 1 N-peptide, TP1NP; beta-C-terminal telopeptide of type 1 collagen, beta-CTX). Results: 1) The average serum level of otoconin-90 in the BPPV group was significantly higher than that in the control group (p < 0.05), whereas both the BMD T scores and serum 25-OH Vitamin D levels of the BPPV group were significantly lower than those of the control group (p < 0.05). 2) There was a strong positive correlation between serum otoconin-90 and age (r = 0.44, p < 0.05) and a moderate negative correlation between otoconin-90 and the bone metabolism indices OC (r = -0.33, p > 0.05), 25-OH Vitamin D (r = -0.35, p > 0.05), and TP1NP (r = -0.30, p > 0.05). 3) Logistic regression analysis showed that serum otoconin-90 level was an independent risk factor for BPPV (odd ratio = 0.998, 95% confidence interval 0.997-0.999, p < 0.01). Conclusion: A correlation between BPPV and abnormal bone metabolism was found. Moreover, otoconin-90 could serve as a research tool for BPPV.