Recently fled asylum seekers generally live in stressful conditions. Their residency status is mostly insecure and, similar to other immigrants, they experience stress due to acculturation. Moreover, they often suffer from traumatization and posttraumatic stress disorder (PTSD). All of these factors can result in chronic maladaptive biological stress responses in terms of hyper- or hypocortisolism and, ultimately, illness. We believe the current study is the first to compare hair cortisol concentration (HCC) of recently fled asylum seekers with PTSD to those without PTSD, and to compare HCC of asylum seekers to HCC of permanently settled immigrants and non-immigrant individuals. HCC of the previous 2 months was compared between 24 asylum seekers without PTSD, 32 asylum seekers with PTSD, 24 permanently settled healthy Turkish immigrants and 28 non-immigrant healthy Germans as the reference group. Statistical comparisons were controlled for age, sex and body mass index. No significant difference in HCC was found between asylum seekers with and without PTSD. However, the asylum seekers showed a 42% higher HCC than the reference group. In contrast, the permanently settled immigrants exhibited a 23% lower HCC than the reference group. We found relative hypercortisolism in recently fled asylum seekers, but no difference between persons with and without PTSD. These findings add to the very few studies investigating HCC in groups with recent traumatization and unsafe living conditions. Contrary to the findings in asylum seekers, permanently settled immigrants showed relative hypocortisolism. Both hyper- and hypocortisolism may set the stage for the development of stress-related illnesses.