Osteopathy, as a major feature of homozygous beta-thalassaemia, is a multifactorial disorder, not fully understood. We studied the lumbar vertebrae of 48 patients using Dual-Energy X-ray Absorptiometry (DXA) and Quantitative Computed Tomography (QCT), and we focused on structural properties, assessed by High Resolution Computed Tomography (HRCT). Bone Mineral Density (BMD) values were expressed as Z-scores and the results were correlated. The effect of age, sex, and type of thalassaemia and hormonal factors on BMD was assessed. We estimated, with HRCT, the cortex integrity and the number and thickness of trabeculae; the latter were classified to a three-grade scale. Our results showed the overall prevalence of osteoporosis to be 44% with DXA and 6% with QCT. Both techniques revealed an inverse correlation between age and BMD, whereas hormonal factors demonstrated associations with QCT and DXA measurements. The correlation coefficient between DXA's BMD and QCT's trabecular BMD was 0.545 (P < 0.001) whereas the corresponding value for Z-scores was r = 0.491 (P < 0.001). The classification of the patients into normal, osteopenic and osteoporotic categories, using QCT's Z, was in better agreement with the assignment based on trabecular number (K = 0.209, P = 0.053) than the classification using DXA's Z (K = 0.145, P = 0.120). Cortex evaluation by HRCT showed discontinuity in 15 patients. Both methods indicate a progression of osteoporosis with age. Hormonal deficiency is associated with thalassaemic osteoporosis whereas the visual estimation of cortex indicates that Thalassaemia Intermedia (TI) patients could be more affected than Thalassaemia Major (TM). Using the trabecular number as an indicator of osteoporosis, it seems that QCT may evaluate osteopathy better than DXA. Since the former has the ability to measure trabecular and cortical BMD separately, it could give early indication of which changes more rapidly and to what degree.