Background Low bone mineral density (BMD) has been reported in HIV-infected women and men. Methods We analysed cross-sectional BMD measured by regional dual X-ray absorptiometry at the lumbar spine (LS) and femoral neck (FN) in 152 HIV-negative and 274 HIV-positive (HIV+) women, adjusted for traditional low BMD risk factors. Results BMD was significantly lower in protease inhibitor (PI) users than in all other groups, and highest in HIV-negative women. In multivariate analyses the prevalence of T-score <-1.0 was significantly higher in the HIV+ women naive to antiretroviral therapy (ART; odds ratio [OR] 4.36, 95% confidence interval [CI] 1.61, 11.8) and the women receiving PI-containing HAART (OR 3.72, CI 1.43, 9.68), with a non-significant difference in non-PI HAART users (OR 2.43, CI 0.92, 6.45), compared with HIV-negative women. In pair-wise adjusted comparisons, BMD was lower in ART-naive than in HIV-negative women (1.22 versus 1.30 g/cm2 at LS; P=0.004), in PI compared with non-PI HAART users (1.00 versus 1.05 g/cm2 at FN; P=0.014) and with those ART-naive (1.00 versus 1.03 g/cm2 at FN; P=0.146). Potential confounders, including duration of ART, prior treatment regimens and traditional risk factors for low BMD did not explain these differences. Longer lopinavir use was significantly correlated with lower BMD (r2=-0.39, P=0.024 and r2=-0.46, P=0.006 at LS and FN, respectively) and longer efavirenz use with higher BMD (r2=+0.32, P=0.004 at FN). Conclusions HIV infection was associated with lower BMD in women, independent of the traditional risk factors for low BMD. PI-containing HAART compared with non-PI-containing HAART, and longer lopinavir use, were both associated with lower BMD, and efavirenz use was associated with higher BMD.