To evaluate bone loss in the early- and late-stage ankylosing spondylitis (AS) patients using posteroanterior (PA) and lateral lumbar and femoral bone mineral density (BMD) measurement methods. Eighty-six AS patients and 50 control subjects were enrolled. PA spine, lateral spine, and femur BMD values of patients and controls were measured. The presence of any syndesmophytes or compression fractures was determined. Patients were divided as early (< 10 years) and late stage (a parts per thousand yen10 years) according to the onset of the inflammatory pain. Mean PA spinal BMD was similar in patients and controls (p = 0.460). Femoral and lateral spine BMD values were significantly lower in patients (p = 0.012 and p = 0.001). When comparing early- and late-stage AS groups, mean PA spinal BMD was found to be lower in the early group (p = 0.005), while femoral and lateral spinal values were lower (although statistically not significant) in the late group. At least one compression fracture was present in 28 % of patients. Although not statistically significant, mean PA spinal BMD was higher in those with fractures. Femoral and lateral spinal BMD values were significantly lower in the fracture group (p = 0.034 and p = 0.004). Lateral spinal BMD values were significantly lower in patients with syndesmophytes (p = 0.004). Bone loss is increased in AS compared with control subjects. The BMD measurement at the lateral lumbar spine reflects bone loss and fracture risk better than PA spine and femoral measurements.