Background: When newborn sepsis occurs, the pathogen may trigger an uncontrollable systemic inflammatory response that results in oxidative damage. Melatonin released naturally, which acts as a safe antioxidant and free radical scavenger in newborns. Aim of the work was to evaluate the significance of plasma melatonin level in early diagnosis of late onset sepsis neonatal sepsis. Patients and Methods: 58 full-term babies were included in a case-control study at Zagazig University's neonatal intensive care unit. Twenty-nine newborns in the patient group had complete clinical and biochemical signs of sepsis. The control group included twenty-nine newborns with no clinical or biochemical signs of sepsis. Melatonin level was measured by ELISA, and a septic work-up was done for all the patients. Results: The best cutoff plasma melatonin level in the diagnosis of late onset sepsis was16.2 pg/ml with an area under the curve of 0.97, a sensitivity of 92.6%, specificity of 86.4%, positive predictive value of 90.5 %, negative predictive value of 87% and over all accuracy of 88.6%. Conclusion: A significant elevation of endogenous plasma melatonin level was found in late-onset neonatal sepsis, so early identification of late-onset sepsis could considerably help cases by allowing both the prevention of complications and avoiding multiple drug resistance.