The worldwide financial crisis during recent years has raised concerns of negative public health effects. This is notably evident in southern Europe. In Greece, where the financial austerity has been especially pronounced, the prevalence of mental health problems including depression and suicide has increased, and outbreaks of infectious diseases have risen. The main objective in this study was to investigate whether different indicators of health and stress levels measured by a new biomarker based on cortisol in human hair were different amongst comparable Greek and Swedish young adults, considering that Sweden has been much less affected by the recent economic crises. In this cross-sectional comparative study, young adults from the city of Athens in Greece (n = 124) and from the city of Linkoping in Sweden (n = 112) participated. The data collection comprised answering a questionnaire with different health indicators and hair samples being analyzed for the stress hormone cortisol, a biomarker with the ability to retrospectively measure long-term cortisol exposure. The Greek young adults reported significantly higher perceived stress (p<0.0001), had experienced more serious life events (p = 0.002), had lower hope for the future (p<0.0001), and had significantly more widespread symptoms of depression (p<0.0001) and anxiety (p<0.0001) than the Swedes. But, the Greeks were found to have significantly lower cortisol levels (p<0.0001) than the Swedes, and this difference was still significant in a multivariate regression (p<0.0001), after adjustments for potential intervening variables. A variety of factors related to differences in the physical or socio-cultural environment between the two sites, might possibly explain this finding. However, a potential biological mechanism is that long-term stress exposure could lead to a lowering of the cortisol levels. This study points out a possible hypothesis that the cortisol levels of the Greek young adults might have been suppressed and their HPA-axis down-regulated after living in a stressful environment with economic and social pressure.