Within the normal inner ear, there are elements that belong to the immune system. Different inner ear disorders can be explained by autoimmune mechanisms, affecting both humoral and cellular immunity. Melatonin, the principal hormone of the pineal gland, modulates the immune system and extensively participates in the autoimmune processes related to type II collagen. Therefore, we have studied the presence of melatonin in rat cochlea, proving that its concentrations change depending on lighting conditions. Rats show high levels when confined to darkness and low levels when subject to continuous light exposure. The results correlate with the concentration of melatonin in peripheral circulation. Further experimental and clinical studies are necessary to clarify the role and the possible therapeutic applications of melatonin.