PTSD is associated with metabolic comorbidities; however it is not clear how the neuroendocrine disturbances affect metabolism. To analyze this we employed a systems biological approach using an integrated mathematical model of metabolism, HPA axis and inflammation. We combined the metabolomics, neuroendocrine, clinical lab and cytokine data from combat-exposed veterans with and without PTSD, to characterize the differences in regulatory effects. We used the pattern of fold change in metabolites representing pathway level differences as reference for metabolic control analysis (MCA) using the model. MCA revealed parameters constituting the HPA axis, inflammation and GPCR pathway that yielded metabolic dysfunction consistent with PTSD. To support this, we performed causal analysis between regulatory components and the significantly different metabolites in our sample. Causal inference revealed that the changes in glucocorticoid receptor sensitivity were mechanistically associated with metabolic dysfunction and the effects were jointly mediated by insulin resistance, inflammation, oxidative stress and energy deficit.Post-traumatic stress disorder (PTSD) is defined by a complex set of criteria including intrusive reminders, fear memories, emotional distress, hypervigilance and exaggerated startle responses that develop and persist after an exposure to trauma 1 . Multiple physiological systems at the neuronal, metabolic, inflammatory, genomic and epigenomic levels are known to be affected in PTSD 2,3 . Previous studies from our PTSD Systems Biology consortium reported associations between PTSD and insulin resistance 4 , inflammation 5 , reduced mitochondrial copy number 6 , and lower methylation of the glucocorticoid receptor (NR3C1) gene 7 in the same cohorts assessed in the present study. The data from animal models and humans with PTSD reveal association between inflammation and metabolic syndrome 8 . Analysis of metabolomics have revealed metabolic changes consistent with dysregulation in mitochondrial functioning in PTSD 9 . Another study reported differences in the mitochondrial DNA (SNPs) located in NADH dehydrogenase and ATP synthase genes in PTSD 10 . Variants of mitochondrial genes and dysregulation of their associated networks have been reported in the postmortem brains of patients with PTSD 11 .One of the major physiological regulatory axes, Hypothalamic-Pituitary-Adrenal (HPA) axis is implicated in the pathogenesis of PTSD and associated metabolic disorders 12,13 . The HPA axis relays stress signals from the brain to peripheral parts through the release of glucocorticoids (GCs) and catecholamine hormones. GCs orchestrate the activities of several physiological functions through glucocorticoid receptor (GRs) signaling. Therefore, the feedback sensitivity of GC signaling among other factors can influence downstream effects of stress exposure. GR signaling is regulated at transcriptional and epigenetic levels and is dysregulated in HPA axis associated disorders 14 . Recent studies have highlighted the asso...