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Background: Recent research indicates that both endocannabinoids (eCB) and heart rate variability (HRV) are associated with stress-induced experiences. However, these underlying mechanisms are not elucidated. The present study aims to investigate whether exposure to acute and chronic stress conditions can give rise to measurable changes, both to the peripheral eCB ligands and HRV. Methods: Thirteen candidates under intense preparation for their enlistment in the Hellenic Navy SEALs (HNS) participated in the study. All subjects underwent mental state examination, while HRV variables in time and frequency domain recordings were acquired. Furthermore, at baseline and 30 days after prolonged and intensive physical exercise, hair was collected to measure eCB ligands, such as anandamide (AEA), 2-arachidonoylglycerol (2-AG), and the N-acyl ethanolamine (NAE) molecules: palmitoylethanolamide (PEA) and oleoylethanolamide (OEA). Results: Comparing basal hair concentrations of eCB ligands before and after intense physical exercise, we found that AEA, PEA, and OEA were notably increased, whereas no differences were observed regarding the ligand 2-AG. Furthermore, there were observed associations between the concentrations of peripheral eCB ligands, both at baseline and after the prolonged physical exercise and the time and frequency domains of HRV. Conclusions: These findings suggest that endocannabinoid–HRV interrelations might share a short-term, and long-term adaptability of the changes in self-regulation associated with stress. Further studies will be required to determine the validity of peripheral eCB signaling and HRV as a biomarker for different aspects of the stress response.

Endocannabinoids and Heart Rate Variability Alterations after Exposure to Prolonged Intensive Physical Exercise of the Hellenic Navy SEALs