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Introduction Circadian rhythm disturbance is associated with neurologic, metabolic, cardiovascular and immune disorders. As the most reliable biomarker of endogenous circadian rhythms, melatonin regulates the sleep-wake cycle and promotes sleep. Studies have demonstrated that saliva and plasma melatonin levels show strong correlations in non-surgical populations. However, the relationship between salivary and plasma melatonin measurements in patients undergoing surgery is unknown. This study will analyse the correlation between the peak concentrations of salivary and blood melatonin in perioperative patients.Methods and analysis In this prospective study, 102 patients scheduled for thoracic or neurosurgical procedures are being enrolled. The primary outcome of this study is to analyse the correlation between the peak concentrations of salivary and plasma melatonin (measured at 04:00 on the first postoperative day) in patients.Ethics and dissemination The study protocol has been approved by the Medical Ethics Committee of Peking University Third Hospital (M2023009). The results of the study will be published in peer-reviewed international journals.Trial registration number The study has been registered at the Chinese Clinical Trial Registry ( www.chictr.org.cn) with identifier ChiCTR2300070470. The latest version of the trial protocol was approved in October 2023.