Abstract : We have studied the influence of the sexual hormone variations throughout the estrous cycle in the Harderian gland. We selected the two phases with the most important differences in the estrous cycle : the estrus, with the highest estrogen level and the diestrus, with the lowest estrogen and highest melatonin levels. Oxidative balance was characterized in both phases, and it was observed that the redox markers are in opposite points in each phase. The highest oxidative damage and low antioxidant response were found in the estrus phase, while the lowest damage and high antioxidant activity was in the diestrus phase. Mitochondrial viability study showed a low mitochondrial population in the estrus, that was evaluated by citrate synthase activity. Massive autophagy and selective autophagy co-exist in the Harderian gland. The key macroautophagy markers, Beclin-1 and the ratio of LC3-II/LC3-1 were higher in the estrus phase. In selective autophagy, Lamp-2a protein expression was observed to be higher in the estrus phase versus the diestrus phase.