Cumulative exposure to stress over a long period can negatively impact an individual’s health. Significant advancements in biomarkers of chronic stress have been made, with the use of fingernails recently explored. Cross sectional data from the Australian Aboriginal Birth Cohort (Indigenous) and Top End Cohort (non-Indigenous) were used to investigate the associations (sociodemographic and emotional) of fingernail cortisol in Indigenous and non-Indigenous young adults. Details on sociodemographic (age, gender, and Indigenous identification), smoking and alcohol use, emotional wellbeing, and emotional stress (perceived stress and stressful events), and fingernail samples were obtained face-to-face. Fingernail samples were analyzed for 179 Indigenous and 66 non-Indigenous participants (21–28 years). Indigenous participants were subjected to higher rates of stressful events compared to non-Indigenous (Median 6.0; interquartile range (IQR) 4, 9 vs. 1.0; IQR 0, 2; p <.001). Median cortisol levels were similar between Indigenous and non-Indigenous participants (4.36 pg/mg; IQR 2.2, 10.0 vs. 3.87 pg/mg: IQR 2.0, 9.7; p =.68). However, Indigenous participants had a higher cortisol level on adjustment for emotional distress and exposure to stressful events (Geometric Mean 1.82; 95CI: 1.07–3.09), with a negative association with increasing number of stressful events (Geometric Mean 0.94; 95CI 0.90, 0.99). Collection of fingernails was an easily conducted, well-tolerated method to measure stress markers in this multicultural cohort. Indigenous young adults experienced a high number of stressful events which was associated with a lowering of fingernail cortisol levels.Lay abstract Chronic stress can impact negatively on health and emotional wellbeing. A fingernail sample provided a culturally acceptable, noninvasive method of measuring chronic stress in Indigenous and non-Indigenous young adults. Cortisol levels, a marker of chronic stress, were different between Indigenous and non-Indigenous young adults and were influenced by emotional status and occurrence of multiple stressful events.