Automatic milking systems (AMS), consisting of one or more automatic milking units in a loose-house system, have become increasingly common in recent years. The milking process as well as the management in AMS differ from conventional systems and may influence the health and welfare of cows in various ways. For example, the daily rhythm and herd synchronization is influenced as cows in the AMS get milked singly at any time of day. In this particular study Dairy cows’ stress responses during normal successful milking in a herringbone milking parlour (HMP) were compared with their responses during normal successful voluntary milking in an automatic unit. The study used 42 cows: 12 Simmental and 11 Brown Swiss in the AMU, and 10 Simmental and 9 Brown Swiss in the HMP. After effects of milk yield, day of lactation and time of day had been taken into account, milking lasted longer in the HMP than in AMU. Location of the teats by the robot took longer in Simmental than in Brown Swiss cows. Kicking and stepping with hind legs was less frequent in the AMU than in the HMP. Brown Swiss cows stepped less than Simmental cows in the AMU. There was no difference between groups in heart rate during milking. The AMS group had higher milk cortisol values than the HMP group. This was probably not related to milking itself, but to other aspects of the system, and the absolute values were not very high. In summary, cows showed more behavioural signs of discomfort and aversion in the HMP than in the AMU. Simmental cows may be more vulnerable during milking than Brown Swiss. There were no indications of more stress in the AMU than in the HMP.