The objective of this study is to assess the prevalence and risk in patients with juvenile onset ankylosing spondylitis (JoAS) complicated with low bone mineral density (BMD). A total of 112 children and adolescents with JoAS were enrolled in the study. Bone mass was measured from the lumbar spine and the left proximal femur using dual-energy X-ray absorptiometry. According to the 2007 International Society of Clinical Densitometry definitions, a Z score of less than -2 was termed as "low BMD." Stepwise regression analysis was used to investigate associations between low BMD and disease-related factors including gender, age, weight, height, body mass index, disease duration, HLA-B27 antigen, grades of sacroiliitis, Bath AS Disease Activity Index (BASDAI), Bath AS Functional Index (BASFI), patient global assessment (PGA), spine pain, erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP). Low BMD was found in 18 (16.1 %) cases in at least one of the two measured regions. Lumbar spine BMD had negative correlations with BASDAI, BASFI, spine pain, ESR, and CRP (P < 0.05). Hip BMD significantly negatively correlated with BASDAI and PGA (P < 0.05). In conclusion, patients with JoAS are likely to develop low BMD, which may be related to high disease activity.