Homocystinuria (HCU) due to deficiency of cystathionine beta-synthetase is associated with increased plasma levels of homocysteine and methionine and is characterized by developmental delay, intellectual impairment, ocular defects, thromboembolism and skeletal abnormities. HCU has been associated with increased risk for osteoporosis in some studies, but the natural history of HCU-related bone disease is poorly understood. The objective of this study was to characterize bone mineral density (BMD) measured by dual energy X-ray absorptiometry (DXA) in a multi-center, retrospective cohort of children and adults with HCU. We identified 19 subjects (9 males) aged 3.5 to 49.2 years who had DXA scans performed as a part of routine clinical care from 2002–2010. The mean lumbar spine (LS) BMD Z-score at the time of first DXA scan in this cohort was −1.2 (± SD of 1.3); 38% of participants had low BMD for age (as defined by a Z-score ≤ −2). Homocysteine and methionine were positively associated with LS BMD Z-score in multiple linear regression models. Our findings suggest that low BMD is common in both children and adults with HCU and that routine assessment of bone health in this patient population is warranted. Future studies are needed to clarify the relationship between HCU and BMD.