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Contrary findings exist on the consistency between hair cortisol and salivary cortisol in assessing the basal activity of the hypothalamic-pituitary-adrenal (HPA) axis. The mismatches in temporal characteristic and the indices of hair and salivary cortisol might be potential reasons for the inconsistency. The aim of this study was to investigate the consistency between hair and salivary levels in cortisol and cortisone by directly examining the correlation between hair level and salivary level with different temporal characteristics (acute, short-term and long-term levels) and reflecting different HPA functions (basal level and reactivity level) in the well-matched time span.A longitudinal design within a five-week period was conducted in a sample of 44 healthy female college students (mean age: 18.8 yrs.; age range: 18–22 yrs) of Han nationality with the exclusion criteria, such as use of oral contraceptives or glucocorticoids and bleached hairs, etc. Four saliva samples (awakening, awakening + 30 min, awakening + 4 h and awakening + 9 h) were collected from an identical participant on three separate days with an interval of one week and 1-cm hair segment nearest to the scalp was collected two weeks later after completing saliva collection. Cortisol and cortisone in saliva and hair were simultaneously measured with high performance liquid chromatography tandem mass spectrometry.There were significantly moderate correlations in cortisol and cortisone between hair level and three-day average of single-day salivary level, but low to moderate correlations between hair level and single-point and single-day salivary level. Hair cortisol and cortisone were unrelated to single-day level and three-day average of diurnal slope and cortisol awakening response of salivary cortisol and cortisone, respectively.The considerable consistency between hair level and long-term salivary level in cortisol and cortisone implies that cortisol and cortisone in hair are valid biomarkers of cumulative exposure of cortisol and cortisone to retrospectively reflect long-term basal activity of the HPA system.