Developments in affective neuroscience and behavioural science during the last 10-15 years have together made it increasingly apparent that sentient animals are potentially much more sensitive to their environmental and social circumstances than was previously thought to be the case. It therefore seems likely that both the range and magnitude of welfare trade-offs that occur when animals are managed for human purposes have been underestimated even when minimalistic but arguably well-intentioned attempts have been made to maintain high levels of welfare. In light of these neuroscience-supported behaviour-based insights, the present review considers the extent to which the use of currently available reference standards might draw attention to these previously neglected areas of concern. It is concluded that the natural living orientation cannot provide an all-embracing or definitive welfare benchmark because of its primary focus on behavioural freedom. However assessments of this type, supported by neuroscience insights into behavioural motivation, may now carry greater weight when used to identify management practices that should be avoided, discontinued or substantially modified. Using currently accepted baseline standards as welfare reference points may result in small changes being accorded greater significance than would be the case if they were compared with higher standards, and this could slow the progress towards better levels of welfare. On the other hand, using "what animals want" as a reference standard has the appeal of focusing on the specific resources or conditions the animals would choose themselves and can potentially improve their welfare more quickly than the approach of making small increments above baseline standards. It is concluded that the cautious use of these approaches in different combinations could lead to recommendations that would more effectively promote positive welfare states in hitherto neglected areas of concern.