Modern warfare has resulted in a high percentage of military personnel experiencing mild traumatic brain injury (mTBI) and blast exposure due to training accidents and other occupational risks. These ‘mild’ injuries are thought to decrease mental resilience and increase the risk of developing maladaptive physiological processes. This study compared saliva neuroendocrine biomarkers in Canadian Armed Forces Personnel (n=108) over three unique stress environments: pre-deployment, deployment in Afghanistan and post-deployment reintegration. At each timepoint, participants provided saliva samples which were assessed for amylase, Chromogranin A (CgA) C-reactive protein (CRP), cortisol and testosterone. Participants were grouped based on their baseline TBI history (i.e. mTBI vs none), with further subgrouping for (a) both blast+mTBI: (b) blast only: (c) mTBI only: (d) no history of blast or mTBI. Two-way repeated measures ANOVAs were used to compare groups over time. Significant differences were found in amylase, CgA, CRP and testosterone concentrations (all p<0.05), with significant interactions between group, timepoint and sex (p<0.05). Notably, these differences were driven by the blast and blast+concussion subgroups for amylase and CgA, while CRP and testosterone levels were elevated over time only in the mTBI subgroup. No differences were found in cortisol concentrations at any timepoint. These findings suggest that blast and mTBI may cause differential responses to stress and influence biological resilience or susceptibility. Our findings provide unique insight into the mechanistic changes which occur during and following high stress military environments in at-risk populations, suggesting that blast and mTBI should be considered and treated as separate entities.