Hair cortisol concentrations (HCC) are increasingly recognized as an integrated measure of the systemic cortisol secretion. Yet, we still know very little about confounding effects on HCC in animals. The present study therefore used hair from semi-wild and zoo living chimpanzees to investigate (1) intra-individual variability of HCC (body-region effect), and (2) the stability of HCC along the hair shaft (traditionally called the washout effect). Our results indicate that absolute HCC varied substantially between certain body regions, but a factor analysis revealed that these HCC differences were mainly attributable to one common source of variance. Thus, hair from all body regions provides similar biological signals and can be mixed, albeit at the cost of a lower signal-to-noise ratio. With regard to potential underlying mechanisms, we studied skin blood flow, as observed through thermal images from one chimpanzee. We found the general HCC pattern was reflected in differences in surface body temperature observed in this individual in three out of four body regions. In a separate set of samples, we found first evidence to suggest that the systematic cortisol decrease along the hair shaft, as observed in humans, is also present in chimpanzee hair. The effect was more pronounced in semi-wild than in zoo chimpanzees presumably due to more exposure to ambient weather conditions.