Animal welfare is an issue of great public and scientific interest. In this thesis, physiological and behavioural methods were used to evaluate fear and discomfort in two different species; dogs and goats. In the first study, fear of gun shots and different floor surfaces was investigated in collie dogs. Dogs that were fearful of floors had higher heart rates than dogs that were less fearful. Dogs fearful of gunshots had higher heart rates, haematocrit and plasma concentrations of cortisol, progesterone, vasopressin and β-endorphin, than less fearful dogs, which demonstrates that fear of gunshots is a serious stressor. In the second study, it was shown that housing and company of other animals affects arterial blood pressure, heart rate, and the concentrations of β-endorphin and oxytocin in goats. However, cortisol and vasopressin concentrations did not differ between goats that were tethered respectively loosely housed in pairs. In the dairy industry, the permanent early separation of mother and offspring is of great concern. In the third study, we found no changes in heart rate, arterial blood pressure or plasma concentrations of cortisol, β-endorphin, oxytocin and vasopressin in goats after separation. However, both goats and kids vocalised intensively. In the fourth and fifth studies, kids were either permanently separated, daily separated, or kept full-time with mothers, and were subjected to an isolation test with a dog bark at two weeks and two months of age, and an arena test with a suddenly appearing novel object at two months of age. All kids had similar growth rates. Kids kept with their mothers showed more hiding behaviours at two weeks, and early separated kids were more active with another kid. Early separated kids also deviated most in the isolation test at two weeks by reducing their vocalisation earlier and having a higher heart rate before and after dog barking, and at two months by having higher heart rate throughout the test. Daily separated kids bleated comparatively more at two weeks, decreased their heart rate after dog bark and showed the strongest fear reaction in the arena test at two months. In conclusion, it is important to measure several different physiological and behavioural parameters when assessing animal welfare