The association between obstructive sleep apnea (OSA) and bone mineral density (BMD) is poorly elucidated and has contradictory findings. Abdominal computed tomography (CT) for other indications can provide a valuable opportunity for osteoporosis screening. Thus, we retrospectively explored the association between OSA and BMD by examining abdominal CT vertebrae images for a multitude of conditions and indications. We included 315 subjects (174 with OSA and 141 without OSA) who performed at least two CT scans (under similar settings). Both groups had a similar duration between the first and second CT scans of 3.6 years. BMD decreased in those with OSA and increased age. A multivariate linear regression indicated that OSA is associated with BMD alterations after controlling for age, gender, and cardiovascular diseases. Here, we report that OSA is associated with BMD alterations. Further studies are required to untangle the complex affect of OSA on BMD and the possible clinical implications of vertebra-depressed or femoral neck fractures.