HIV-infected patients are at high risk for bone mineral density (BMD) loss. The present study was designed to provide information on characteristics of BMD abnormalities in Japanese HIV-1-infected patients and risk factors involved in worsening of BMD. A total of 184 Japanese HIV-1-infected men were studied with a dual-energy X-ray absorptiometry scan (DXA) at the lumbar spine and femoral neck. Multivariate logistic regression models were used for comparison of the impact of risk factors on BMD loss. Osteopenia and osteoporosis were diagnosed in 46% and 10% of the patients at lumbar spine, and 54% and 12% at femoral neck, respectively. In logistic analysis, factors associated with low BMD at both lumbar spine and femoral neck were long-term treatment with a protease inhibitor (PI) [odds ratio (OR) 1.100 and 1.187 per 1 year increase of PI use; 95% confidence interval (CI) 1.003-1.207 and 1.043-1.351; p=0.042 and 0.009, respectively] and a low body mass index [OR: 0.938 and 0.852, CI 0.892-0.992 and 0.783-0.927; p=0.024 and <0.001, respectively]. Patients who discontinued PI had a significantly higher BMD than those who currently use PI at lumbar spine (t score -0.8 vs. -1.3, p=0.04) but not at femoral neck (-1.3 vs. -1.5, p=0.38). In HIV-infected Japanese patients, the duration of treatment with PI correlated significantly with BMD loss. Discontinuation of PI is a promising option in the treatment of BMD loss since it allows recovery of BMD, especially in the lumbar spine.