Research has frequently linked perceived stress with changes in subjective and objective measures of ill health; however, additional assessment should consider the physiological mechanisms mediating these effects. This study investigated whether differential patterns of cortisol secretion might partially mediate perceived stress related disparities in common health complaints in young, otherwise healthy individuals. To capture the kinds of health complaints commonly reported in this population, the Pennebaker Inventory of Limbic Languidness (PILL) was selected. To capture important parameters of the diurnal profile, cortisol was sampled at waking, 30 minutes post waking, 1200 h and 2200 h on three consecutive weekdays. Results revealed flatter diurnal cortisol slopes and elevated mean diurnal output (characterised by HPA hyperactivity in the evening) for participants in the higher stress group. Participants that reported higher perceived levels of stress also reported experiencing common health complaints with markedly greater frequency; however, these disparities were abolished when mean diurnal output of cortisol was statistically controlled. While dysregulation of basal HPA activity has been implicated in the aetiologies of chronic illness, findings reported here implicated hypersecretion of cortisol as one physiological pathway, partially mediating perceived stress related disparities in the kinds of common health complaints that typically affect young, otherwise healthy individuals.