The heart rate variability (HRV) parameters of dairy cows were monitored during parlour (PARL) and the later installed automatic (AMS) milking on a small-scale commercial dairy farm in Hungary. The aim of the study was to assess stress in relation to the type of milking and the frequency of human interaction. Parlour milking involved regular moving and crowding of the animals with frequent human interaction, which were much less frequent in automatic milking. The first phase of the study was conducted prior to the changeover [n = 27] and the second two months afterwards [n = 19 (of the cows from the first phase)]. Heart rate (HR) was recorded by the Polar RS800 CX recording system. HRV parameters indicative of sympathovagal balance were calculated for periods of lying and standing in the barn, waiting before milking and milking, respectively. Morning and evening faecal glucocorticoid concentrations were also measured. Fear of humans was tested by an avoidance distance test. Baseline HRV parameters showed no difference (P > 0.05) between the two systems. In the periods before, during and after milking a higher sympathetic tone was detected in cows in the PARL phase. Mean faecal glucocorticoid concentrations were higher at the time of parlour milking. The avoidance distance did not differ between the two phases. The results suggest that automatic milking might be less stressful for cows than parlour milking, possibly due to the shorter duration of restraint after milking and the less frequent human interaction.