Severe mental illness (SMI) is associated with a marked increase in mortality, both from natural and unnatural causes. Patients may be subject to accelerated aging and an increased disposition for developing chronic somatic disease. One possible contributory cause to this may be chronic hyperactivity of the hypothalamus-pituitary-adrenal (HPA)-axis and subsequent increased levels of cortisol. This study analyzed hair cortisol concentrations (HCC) using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) in hair samples from forensic autopsies of patients with SMI, validated via health registry data. Results: HCC was not associated with a particular diagnosis or increased in patients compared with decedents without SMI. HCC was higher in decedents who had been prescribed psychotropic medication, especially SSRI and benzodiazepines. HCC was not associated with a history of coerced admissions or high number of days of admission. Future studies evaluating HCC as a proxy marker for stress should consider including medication history as a covariate. Reference ranges for healthy adults using standardized methods are needed in order to provide better interpretation of patient HCC.