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OBJECTIVE Hair cortisol is a promising new biomarker of retrospective systemic cortisol concentration. In this study, we compared hair cortisol concentrations in patients with newly diagnosed bipolar disorder (BD), their unaffected first-degree relatives and healthy individuals and identified potential predictors of hair cortisol concentrations in patients with BD. METHOD In a cross-sectional design, we compared hair cortisol concentrations in 181 patients with newly diagnosed/first episode BD, 42 of their unaffected first-degree relatives and 101 healthy age- and sex-matched individuals with no personal or first-degree family history of affective disorder. In patients with BD, we further investigated whether medication- and illness related variables, as well as measures of stressful life events in the preceding 12 months and childhood trauma, were associated with hair cortisol concentrations. RESULTS Hair cortisol concentrations were 35.1% (95%CI: 13.0-61.5) higher in patients with BD (P = 0.001) compared with healthy individuals in models adjusted for age and sex. Hair cortisol concentrations in unaffected first-degree relatives did not differ from healthy individuals (P = 0.8). In patients, neither medication, illness duration nor stress related variables were associated with hair cortisol concentrations. CONCLUSION We found elevated hair cortisol concentrations in patients newly diagnosed with BD indicating the presence of physiological stress in early stages of BD.