Various stressors activate the hypothalamo-pituitary-adrenal axis (HPA-axis) that stimulates adrenal secretion of glucocorticoids, thereby playing critical roles in the modulation of immune responses. Transcriptional regulation of nuclear genes has been well documented to underlie the mechanism of glucocorticoid-dependent modulation of cytokine production and immune reactions. Glucocorticoids also regulate inflammatory responses via non-genomic pathways in cytoplasm and mitochondria. Recent studies have revealed that glucocorticoids modulate mitochondrial calcium homeostasis and generation of reactive oxygen species (ROS). Although redox status and ROS generation in inflammatory cells have been well documented to play important roles in defense against pathogens, the roles of glucocorticoids and mitochondria in the modulation of immunological responses remain obscure. This review describes the role of stress-induced activation of the HPA-axis and glucocorticoid secretion by the adrenal gland in mitochondria-dependent signaling pathways that modulate endotoxin-induced inflammatory reactions and innate immunity.