Fragility fractures risk is increased among HIV infected patients. Bone microstructure alterations, in addition to bone mineral density (BMD) reduction, might be responsible for the increased risk. The aim of this study was to determine the prevalence of vertebral fractures (VFs) and their association with trabecular bone score (TBS), an indirect index of bone microstructure, in a cohort of HIV-infected subjects. One-hundred and forty-one HIV-infected patients (87% males, median age 43 years, 94% on stable antiretroviral therapy with undetectable viral load) underwent viro-immunological and bone metabolism biochemical screenings. Lumbar TBS and BMD at femoral neck, total hip, and lumbar spine, were measured with dual-energy X-ray absorptiometry (DXA). VFs were identified using the semiquantitative method and quantitative morphometric analysis from thoracic and lumbar spine X-ray images. VFs were observed in 19 patients (13.5%). BMD was below the expected range for age in 18 (12.8%) subjects. No significant differences were found stratifying VFs prevalence by BMD, whereas patients with lower TBS showed a higher prevalence of VFs (p = 0.03). In multivariate analysis, TBS was the only factor significantly associated to VFs (OR = 0.56; 95% CI = 0.33-0.96; p = 0.034), with increased fracture risk for lower TBS values. VFs are prevalent and associated with low TBS among HIV-positive patients, whereas no significant association was found with BMD.