Children with beta thalassemia major (BTM) are known to have reduced bone mass which increases incidence of non-traumatic fractures. Few studies have assessed prevalence of fractures and bone health in underprivileged children with BTM. Our objectives were to 1) determine prevalence of fractures in underprivileged Indian children with BTM, 2) assess size corrected bone density and bone geometry using Dual x-ray absorptiometry (DXA) and peripheral quantitative computerized tomography (pQCT) in these children and healthy controls 3) determine predictors of fractures in children with BTM 4) compare differences in bone density between children with BMT with and without fractures. Bone mineral content and areal bone mineral density (aBMD) of lumbar spine and whole body and vertebral fracture assessment (VFA) was performed by DXA in 334 children (3–18 years, 167 BTM + 167 controls). Volumetric BMD (vBMD) and bone geometry were assessed by pQCT (subset, 70 BTM, 70 healthy) at distal radius. Children with BTM had higher prevalence of vertebral and long bone fractures (p < 0.05). DXA aBMD was lower in children with BTM (p < 0.05), whereas, lumbar spine bone mineral apparent density (LSBMAD) was higher (p > 0.05). Children with BTM had lower total distal radial vBMD, cortical vBMD and strength strain index (SSI) at 66% site whereas, distal radial trabecular vBMD at 4% was higher (p < 0.05). On height adjustment, children with BTM had lower muscle area and cortical thickness and higher marrow area (p < 0.05) at 66% site. Age, body size, total body less head (TBLH) aBMD and strength strain index (SSI) were important predictors of fractures in children with BTM. Thus, children with BTM had higher prevalence of non-traumatic fractures. Despite lower areal and volumetric densities, they had higher LSBMAD and trabecular densities which may be attributed to erythroid hyperplasia and iron deposition due to inadequate transfusion and chelation. As LSBMAD is raised in these children, it is unlikely to identify BTM subjects at risk of fracture;​ VFA thus maybe useful in identifying asymptomatic vertebral fractures.