In a conventional milking system, two to three times a day, cows are driven into the milking parlor. However, dairy barns are now converting to an automatic milking system (AMS), which allows the cows to voluntarily enter the parlor when they so choose to. The aim of this study was to determine the physiological impact on cows when switching from a conventional to an automatic milking system. The variables recorded were milk composition and yield, heart rate, cortisol (via feces). The first time cows entered the AMS, but were not milked, their heart rate rose approximately 35 beats per minute more than levels recorded in the conventional milking parlor. The first milking was performed on the eighth visit to the AMS and by this time the heart rate had returned to levels seen in the conventional milking parlor. There was a decrease in milk yield during the transition. Milk yields dropped between 8 to 96% (average of 68%) of yields from the previous milking in the conventional parlor. The concentration of cortisol metabolites in the feces remained unchanged during the transition between the two systems. To test the relationship between how the cow was coping and the activity level of the adrenal cortex, and ACTH challenge was performed. Cows that had higher cortisol levels, which means the adrenal cortex is more active, were the cows that had during the first milking in the AMS had lower heart rate elevations, and whose milk yield were only minimally depressed. These results illustrate that there is a wide variation in how the cows copes with the transition between a conventional to an automatic milking system.