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Introduction Military field training causes stress due to individual factors, physical strain, cognitive tasks, environmental factors, sleep deprivation, energy deficit and psychological factors. The purpose of this study was to investigate the stress induced by military field training measured objectively and subjectively in young military conscripts. Associations of the changes in studied variables were also investigated.Methods Participants’ (49 men, age 20±1 years) nocturnal and morning heart rate variability, selected hormonal and metabolic status, physical activity, perceived exertion and amount of sleep were measured before the 3-week military field training, periodically during the training (shooting and combat training periods) and 4–5 days after the end of the training.Results Nocturnal and morning heart rate, serum cortisol and sex hormone-binding globulin concentrations, creatine kinase activity, rate of perceived exertion and NASA Task Load Index increased, while testosterone, testosterone/cortisol ratio and insulin-like growth factor 1 decreased. The observed associations between the changes of the studied variables were weak.Conclusions 3-week military field training induced changes in the functions of the autonomic nervous, hormonal and metabolic systems and perceived exertion. The changes may indicate increased physiological and/or psychological stress, signifying changes in anabolic-catabolic balance and overreaching state. Thus, subjectively measured stress corresponds with objectively measured stress, although responses and adaptations differed individually between the participants.