Objective To evaluate the differences of bone mineral density in congenital scoliosis (CS) and adolescent idiopathic scoliosis(AIS) patients compared with age-matched normal control, and quantitatively investigate the microstructure of trabecular bone by micro computer tomography scan in AIS and CS patients. Methods 15 AIS women(12-19 years old, Cobb angle 48?-104?) and 16 CS patients (4 male, 12 female; 13-18 years old, Cobb angle 40?-125?) were recruited into this study. The normal control group consisted of 35 female adolescents(13-16 years old). Bone mineral density was assessed at the lumbar spine and femur neck in every patient before operation and every subject in control group by DEXA. Corrective surgery was indicated to AIS and CS patients and iliac crest biopsy was collected during autograft harvesting. Bone specimens were scanned by micro CT. Results The BMD of lumbar spine and femur neck in AIS patient were significant lower than that in normal control. The BMD and BMC were significantly lower in CS patients compared with normal control. The BMD and BMC of femur neck were significantly lower in CS than that in AIS. The BV/TV in micro CT was significantly associated with the BMD in DEXA. In 3-D model BV/TV value was significantly greater in AIS (19.9%?3.4%) compared with CS (13.3%?3.0%). Significant differences between AIS and CS were also found in the parameters of trabecular thickness and bone surface/bone volume (155.5?54.9) ?m vs (108.1?17.4) ?m and 16.4%?3.3% vs 22.0%?3.4%. Lower trabecular connectivity density and number of trabecular number were observed in CS compared with AIS patient, but without significant difference between them. Conclusion Lower bone mineral density,microstructural abnormalities, lower BV/TV, and weak trabecular bone of ilia were observed in AIS. Both BMD and trabecular bone microstructure in CS patients were lower than those in normal control and AIS patients.