A capacity for the animal to recover quickly from the impact of physical and social stressors and disease challenges is likely to improve evolutionary fitness of wild species and welfare and performance of farm animals. Salience and valence of stimuli sensed through neurosensors, chemosensors and immunosensors are perceived and integrated centrally to generate emotions and engage physiological, behavioural, immune, cognitive and morphological responses that defend against noxious challenges. These responses can be refined through experience to provide anticipatory and learned reactions at lower cost than innate less-specific reactions. Influences of behaviour type, coping style, and affective state and the relationships between immune responsiveness, disease resistance and resilience are reviewed. We define resilience as the capacity of animals to cope with short-term perturbations in their environment and return rapidly to their pre-challenge status. It is manifested in response to episodic, sporadic or situation-specific attributes of the environment and can be optimised via facultative learning by the individual. It is a comparative measure of differences between individuals in the outcomes that follow exposure to potentially adverse situations. In contrast, robustness is the capacity to maintain productivity in a wide range of environments without compromising reproduction, health and wellbeing. Robustness is manifested in response to persistent or cyclical attributes of the environment and is effected via activity of innate regulatory pathways. We suggest that for farm animals, husbandry practices that incorporate physical and social stressors and interactions with humans such as weaning, change of housing, and introduction to the milking parlour can be used to characterise resilience phenotypes. In these settings, resilience is likely to be more readily identified through the rate of return of variables to pre-challenge or normal status rather than through measuring the activity of diverse stress response and adaptation mechanisms. Our strategy for phenotyping resilience of sheep and cattle during weaning is described. Opportunities are examined to increase resilience through genetic selection and through improved management practices that provide emotional and cognitive enrichment and stress inoculation.