Iodine deficiency disorders (IDD) are one of most common nutritional deficiencies in the world. The nuclear analytical methods (ENAA, SRXRF and XRF) were employed to study the effect of iodine deficiency on the metal ion changes during the stage of brain development, combined with biochemical methods. The results show that the distributions of iron, copper and zinc varied to different extent in different brain regions and subcellular fractions of the ID rat brains. These distributional changes of trace elements might be associated with the brain damage caused by the iodine deficiency.