Animal welfare is an important social construct showing that humans recognise the sentient nature of animals and manage them accordingly; however, because the concept differs depending on individual perceptions of the acceptability of different practices and appropriate endpoint measurements, objective evaluation of an animal's welfare state is challenging. A good level of welfare, however, is not achieved merely by the absence of difficulties (e.g. pain, injury, disease, distress) but by the animal's capacity to overcome them. Production-oriented (utilitarian) opinions contend that high production indicates good welfare, as an animal must be healthy and well nourished to achieve it. Although there is truth in this premise, high production can, in itself, result in stresses, with no obvious signs that potentially predispose animals to ill health. The focus of the present paper is on peripartal dairy cattle as it relates to development of better measures for an objective evaluation of welfare state. Advances in high-throughput metabolite (metabolomics) and gene expression (transcriptomics) analysis techniques have enabled the rapid identification of multiple biomarkers that, in combination, reflect the metabolic and immunocompetence functional capacity of the animal. With this knowledge, the effects of management, nutrition, physiological state, and their interactions can be evaluated for their effect on functional capacity. As the links between metabolism, immunology (immunometabolism) and mental state are elucidated, these techniques also offer a means to assess whether the animal also experiences feelings of malaise. Collectively, these measurements, thus, can indicate 'functional welfare', which encompasses biological function, physical state, and some components of mental state as part of animal welfare.