Introduction Elevated levels of cortisol are known to induce various symptoms and diseases, e.g. abdominal obesity, type 2 diabetes, osteoporosis and cardiovascular disease. Measuring serum, saliva and urine cortisol is limited to one time point. Measurement of cortisol in scalp hair is a recently developed method to measure long term cortisol levels. The aim of this study was to investigate whether hair cortisol is a feasible parameter to measure cortisol exposure. Experimental We collected hair samples of 195 healthy individuals, 9 hypercortisolemic and one hypocortisolemic patient and measured hair cortisol levels. Cortisol was extracted from scalp hair using methanol and cortisol levels were measured using a salivary ELISA kit. Measurement of waist and hip circumferences and blood pressure was performed in 46 healthy subjects. Results We found a positive correlation between hair cortisol and both waist circumference ( r = 0.392, p = 0.007) and waist-to-hip ratio (WHR) ( r = 0.425, p = 0.003). No correlations were found between hair cortisol levels and BMI, blood pressure or age. There was no decline in cortisol levels in six consecutive hair segments. Hair cortisol levels were elevated in patients with known hypercortisolism ( p < 0.0001). Conclusions Hair cortisol was positively correlated with WHR, suggesting that hair cortisol reflects cortisol exposure at tissue level, which was also supported by elevated hair cortisol levels in hypercortisolemic patients and concordance between hair cortisol levels and clinical disease course. Cortisol levels in hair are slightly influenced by hair treatment but not by natural hair colour, use of hair products, gender or age.