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Background Saliva cortisol is a possible marker of noise-induced stress and could then mediate the relation observed between exposure to aircraft or road traffic noise and cardiovascular diseases. However, the association between transportation noise and cortisol levels is still unclear. The objective of the study was to investigate the variability of saliva cortisol concentration as an indicator of disturbed hypothalamus-pituitary-adrenal (HPA) axis regulation in relation to long-term aircraft noise exposure. Methods Saliva samples were taken when awakening and before going to bed for 1244 participants older than 18 years of age. Information about health, socioeconomic and lifestyle factors was also collected by means of a face-to-face questionnaire performed at home by an interviewer. Aircraft noise exposure was assessed for each participant’s home address using noise maps. Linear regression models were used to evaluate the effects of aircraft noise exposure on the morning and evening cortisol levels and on the daily variation of cortisol per hour. Results This study suggests a modification of the cortisol circadian rhythm in relation to aircraft noise exposure. This exposure was associated with a smaller variation of cortisol levels over the day, with unchanged morning cortisol levels, but higher cortisol levels in the evening. Conclusions These findings provide some support for a psychological stress induced by aircraft noise exposure, resulting in HPA dysregulation and a flattened cortisol rhythm, thus contributing to cardiovascular diseases.