There is a large literature demonstrating that individuals who have experienced traumatic events have alterations in the hypothalamic-pituitary-adrenal (HPA) axis. However, the existing literature does not address the extent to which these alterations represent pre-existing risk factors for developing psychopathology upon exposure to a significant stressor. In the current study, we examined the relationship between waking salivary cortisol level and physiological, personality, and psychological measures in 60 firefighters and police trainees during training, and then again after exposure to a highly stressful, potentially traumatic event (PTE). Waking cortisol was negatively associated with neuroticism, but positively associated with physiological reactivity to loud tones and fear conditioning when assessed during training. Longitudinally, there were significant negative correlations between pre-PTE waking cortisol and post-PTE negative mood and anxiety symptoms, but a positive correlation (trend) between pre-PTE waking cortisol and post-PTE physiological reactivity during recollection of the PTE. Thus, waking cortisol level may serve to predict divergent types of emotional sequelae following PTEs.