We have previouslyreported that low doses of melatonin inhibit apoptosis in both dexamethasone-treated cultured thymocytes (standard model for the study of apoptosis) and the intact thymus. Here we elucidate the mechanism by which this agent protects thymocytes from cell death induced by glucocorticoids. Our results demonstrate an effect of melatonin on the mRNA for antioxidant enzymes in thymocytes, also showing an unexpected regulation by dexamethasone of these mRNA. Both an effect of melatonin on the general machinery of apoptosis and a possible regulation of the expression of the cell death related genes bcl-2 and p53 are shown not to be involved. We found melatonin to down-regulate the mRNA for the glucocorticoid receptor in thymocytes (glucocorticoids up-regulate their own receptor). The decrease by melatonin of mRNA levels for this receptor in IM-9 cells (where glucocorticoids down-regulate it) demonstrates that melatonin actually down-regulates glucocorticoid receptor. These findings allow us to propose the effects of melatonin on this receptor as the likely mediator of its thymocyte protection against dexamethasone-induced cell death. This effect of melatonin, given the oxidant properties of glucocorticoids, adds another mechanism to explain its antioxidant effects.