OBJECTIVE beta-thalassemia is an important public health problem in the countries bordering the Mediterranean sea. One of the major consequences of this disorder, primarily (due to an ineffective erythropoiesis) or secondarily to blood transfusions (which are necessary for the patient's survival), is iron storage. Applying X-ray microanalysis we wanted to demonstrate the different sites of iron storage in subcellular compartments (mitochondria, cytosol, nucleus, rough endoplasmic reticulum and lipid droplets) and whether there were any other trace elements stored in liver cell. METHODS X-ray microanalysis was performed (at 100 kV in the STEM mode of a Hitachi H7000) on thin sections from specimens of liver biopsies from 6 patients affected by b-thalassemia, during follow-up after bone marrow transplantation. RESULTS Spectra showed no correlation between iron peaks of lysosomes and hepatic iron concentration (HIC) or serum ferritin levels. Iron peaks were also detected in other subcellular compartments such as cisternae of rough endoplasmic reticulum, mitochondria and cytosol. No iron peaks were detected in lipid droplets and no significant iron peaks were found in the nuclei. Traces of copper were almost constantly found in lysosomes and cytosol. CONCLUSIONS These results demonstrated iron storage within subcellular organelles other than lysosomes and highlighted a non-correlation between lysosomal iron peaks and HIC or serum ferritin levels. The presence of traces of copper in the lysosomes and in the cytosol may be correlated with the stronger hypothesis of links in the metabolism of the two elements (iron and copper), as ceruloplasmin is a ferroxidase copper-dependent protein. X-ray microanalysis may become a relevant tool in the localization of iron storage within hepatocytes in the evaluation of the effectiveness of bone marrow transplantation and iron chelation therapy. It also may provide some interesting information about iron metabolism in hepatocytes.