Studies of the brain inform us about the cognitive abilities of animals and hence affect the extent to which animals of that species are respected. However, they can also tell us how an individual is likely to be perceiving, attending to, evaluating, coping with, enjoying, or disturbed by its environment, and so can give direct information about welfare. In studies of welfare, we are especially interested in how an individual feels. Since this depends upon high-level brain processing, we have to investigate brain function. Brain correlates of preferred social, sexual and parental situations include elevated oxytocin in the para-ventricular nucleus of the hypothalamus. Abnormal behaviour may have brain correlates, for example, high frequencies of stereotypy are associated with down-regulated μ and κ receptors and dopamine depletion in the frontal cortex. Such results help in evaluating the effects of treatment on welfare. Some brain changes, such as increased glucocorticoid receptors in the frontal lobes or increased activity in the amygdala, may be a sensitive indicator of perceived emergency. Active immunological defences lead to cytokine production in the brain, vagal nerve activity and sickness effects. Some aspects of brain function can be temporarily suppressed, for example, by opioids when there is severe pain, or permanently impaired, for example, in severely impoverished environments or during depression. Coping attempts or environmental impact can lead to injury to the brain, damage to hippocampal neurons, remodelling of dendrites in the hippocampus, or to other brain disorganisation. Brain measures can explain the nature and magnitude of many effects on welfare.