The left and right sides of the brain are specialized to process information in different ways and to control different types of behaviour. Research on a range of species has shown that the left hemisphere controls well-established patterns of behaviour performed in non-stressful situations, whereas the right hemisphere responds to unexpected stimuli and controls escape and other emergency responses. A body of evidence of lateralization in vertebrates has been established over the last three decades but only recently have domesticated species, other than the domestic chicken, been investigated. Since lateralization of the brain is often manifested as side biases in behaviour, knowledge of lateralization is likely to have particular relevance to the handling and training of domestic animals and to be important in other aspects of their welfare. For example, many species, including horses, are more reactive to novel stimuli presented on their left than on their right side and, since the left eye sends its inputs mainly to the right hemisphere, this reflects the predominant role of the right hemisphere in the expression of emotions and in controlling both flight and fight responses. Moreover, animals that are more fearful and, according to circumstances, more aggressive use their right hemisphere more than the left and often express left eye or limb preferences. Hence, knowledge of limb and eye preferences can assist in detecting individuals that are more fearful and flighty, as well as more likely to suffer high levels of physiological stress. The strength of these side preferences is also important; in dogs, weaker paw preference is associated with noise phobia and stronger bias to use the right hemisphere to process sounds, including vocalisations, is associated with increased emotional reactivity. These and other examples will be discussed to illustrate the relevance of research on lateralization to animal welfare.