Introduction: Radiation is widely used in the treatment of various cancers and in radiological imaging procedures. Ionizing radiation causes adverse effects, leading to decreased quality of life in patients, by releasing free radicals that cause oxidative stress and tissue damage. The sleep-hormone melatonin is a free radical scavenger, and induces several anti-oxidative enzymes. This review investigates the scientific literature on the protective effects of melatonin against exposure to ionizing radiation, and discusses the clinical potential of melatonin as prophylactic treatment against ionizing radiation damage. Methods: A systematic literature search was performed and included experimental or clinical studies written in English that investigated the protective effects of melatonin against gamma or X-ray irradiation in vivo. Studies were excluded if patients were treated with chemotherapy concomitantly. Results: 37 studies were included in the review. All were of experimental case-control design and employed animals. The studies demonstrated that exogenous melatonin reduced oxidative stress and inflammation in all investigated tissues. Furthermore, melatonin increased 30-day survival and protected against radiation enteritis. These protective effects were only documented when melatonin was administered prior to exposure to ionizing radiation. Discussion: This review documents that melatonin effectively protects animals against injury to healthy tissues from ionizing radiation. However, no studies have been performed in humans. If clinical studies can document similar protective effects, melatonin could have a great potential to prevent side effects of radiotherapy for cancer, to protect against increased long-term cancer risk in radiological imaging procedures, and to protect from radiation due to nuclear incidents.