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Simple Summary  This research was carried out to investigate changing stress levels in dairy cows when changing from convention milking to an automatic milking system (AMS). Elevated stress levels can cause problems with immunity and reproduction. Stress in cows can be measured using cortisol levels found in saliva and hair (among others). AMS require fewer herds people and are associated with a higher milking frequency and higher milk yields. In this study, we present short-term and long-term cortisol levels in 10 and 12 cows respectively, over a period of 3–12 months. Hair and saliva samples were obtained with minimal restraint to the cow and analysed in the laboratory. Mixed models were applied to determine the effect of various parameters on cortisol levels. These show that non-lame cows had a reduction in salivary levels after AMS installation. Lameness and pregnancy affected salivary but not hair cortisol. Hair cortisol levels increased after installation, but this effect may have been seasonal. Milk yield increased and udder health improved across the whole herd but there was no change in the poor foot health. Our results show that AMS improves production and is not associated with an increase in cow stress. We recommend that welfare, natural behaviour and foot health are considered when introducing automatic milking systems.    Abstract  Automatic milking systems (AMS) are a low-labour alternative to conventional parlours, with previous studies demonstrating that cows vary in their ability to cope with the change to AMS. Cortisol expression can be combined with other measures to assess stress: saliva and hair have the advantage of requiring minimally invasive sampling. No work has investigated the long-term impact of introduction of AMS. The aims of the study were to assess short-term and chronic stress associated with a change in milking system by measuring salivary and hair cortisol levels and to assess the impact on health and production parameters. Cows from one farm changing their milking system were recruited to the study and sampled for saliva ( n  = 10) and hair ( n  = 12) before and after installation. Cortisol levels were measured using a salivary cortisol enzyme immunoassay kit. Body condition, lameness and milk parameters of the whole herd were regularly assessed. Salivary cortisol showed no diurnal pattern but was affected by lameness and gestation. Non-lame cows showed a reduction in salivary cortisol after AMS introduction ( p  < 0.001). Hair cortisol levels increased after AMS, but it was unclear if this change was seasonal. Milk yield increased by 13% and somatic cell count reduced by 28%. Body condition score was consistently good, but lameness remained high throughout the study. Production values alone do not represent high welfare. The high lameness and associated cortisol levels suggest that cow stress requires consideration when changing milking systems.

Minimally Invasive Markers of Stress and Production Parameters in Dairy Cows before and after the Installation of a Voluntary Milking System