Although major progress has been made during the last 50 years in understanding the causes of, and devising methods to minimise, neonatal mortality and morbidity in farm animals, almost all of this progress has been made without an explicit animal welfare focus. Nevertheless, knowledgeable intervention at birth now markedly reduces the total amount of animal welfare compromise that would otherwise occur. In assessing the degree of welfare compromise in other contexts three orientations are apparent. These emphasise biological function, affective state and natural living. In the present paper the significance of these orientations in an assessment of welfare compromise in newborn lambs, kids, calves, deer calves, foals and piglets, conducted previously, is examined. It is concluded that: 1) it was appropriate to emphasise biological function during the research which improved the management of newborns, but this emphasis was not sufficient to characterise the nature and degree of welfare compromise the newborn might experience; 2) a focus on affective state, and particularly on noxious sensations, more appropriately allowed an initial assignment of different degrees of compromise caused by neonatal breathlessness, hypoxia, hunger, sickness and pain; and 3) the notion that farm animals should be left to fend for themselves in a natural state at the time of birth when knowledgeable intervention would markedly reduce neonatal suffering contradicts our duty to care for the animals in our control. Finally, on-farm assessments of neonatal welfare compromise would be possible, but they would need to allow for the prevalence and severity of each condition, which can vary widely depending on the species and local circumstances.