The assessment of positive emotional states in animals has been advanced considerably through the use of judgement bias testing. JBT methods have now been reported in a range of species. Generally, these tests show good validity as ascertained through use of corroborating methods of affective state determination. However, published reports of judgement bias task findings can be counter-intuitive and show high inter-individual variability. It is proposed that these outcomes may arise as a result of inherent inter- and intra-individual differences as a result of biology. This review discusses the potential impact of sex and reproductive cycles, social status, genetics, early life experience and personality on judgement bias test outcomes. We also discuss some aspects of test design that may interact with these factors to further confound test interpretation. There is some evidence that a range of biological factors affect judgement bias test outcomes, but in many cases this evidence is limited and needs further characterisation to reproduce the findings and confirm directions of effect. It is our proposition that researchers should consider dedicated study on these factors and their impact on judgement biasing. This is needed to confirm effect and investigate mechanisms. Alternately, consideration and reporting of these factors in JBT studies through incorporation in statistical analyses will provide much needed additional data on their impact. These actions will enhance the validity and practical applicability of the JBT for welfare assessment.