The aim of the present study was to investigate physiological effects of highly similar production systems with different degrees of automation by use of urinary catecholamines and cortisol as well as salivary cortisol. Furthermore, it was determined whether the physiological response was related to real-time self-reports in terms of feelings of Positive and negative arousal, physical exertion, and sleepiness. Sixteen healthy women sorting wooden slats participated in the study. The work was highly repetitive and demanded intense concentration and rapid qualified decisions. The women rotated between three production systems with varying degrees of automation. Real-time logbooks were completed and urine was collected five times and saliva seven times on four work-days and on one day off. When working at the most automated production system urinary concentrations of adrenaline and noradrenaline were 14 per cent lower compared to those obtained when working at the other production systems. For salivary cortisol, the profile over the day differed between production systems. The type of production system did not affect urinary cortisol. Feelings of positive and negative arousal were associated with increased concentrations of urinary adrenaline, while sleepiness was associated with lower salivary cortisol. These associations were independent of the relationship between production systems and biomarkers. In conclusion, decreased physiological arousal was observed in response to increased automation and real-time self-reports appeared to be related to specific physiological systems.