Retrieved memories of emotionally laden events are likely to influence the ongoing emotional state and behaviour of animals. If animals consciously experience memories and/or associated emotions, then recall of aversive or pleasurable events will affect their welfare. Even if they do not, retrieval of these (non-conscious/implicit) memories may result in behaviour, such as attempts to escape, that could lead to injury and damage. There is growing evidence that emotionally laden events are more readily stored in memory than neutral ones, and that the neurophysiological basis of this, involving acute elevations of the classic stress hormones and the action of the amygdala, is similar in humans and other vertebrate species. Thus, in humans and animals, emotional memories are likely to be stored as priority information and may readily be retrieved in the presence of relevant cues. If so, an important practical goal is to minimize the chances of negative emotional memories being cued inappropriately, especially for animals in captivity. Disruption of memory formation and retrieval is also important in an animal welfare context. Chronic or very high elevations of stress hormones appear to have both short- and long-term effects on brain structure and function that can interfere with efficient storage of information. Environmental disturbances, including common husbandry procedures, can also disrupt memory formation through retroactive interference effects. Elevated stress levels may both increase the chances of retrieval of negative information while hampering the retrieval of positive or neutral information. These effects may lead to poor learning abilities, selective or disrupted memory retrieval, and consequent inappropriate behaviour with adverse welfare consequences. If we understand them, we may be able to recommend housing or husbandry procedures that minimize the likelihood of their occurrence.