Brain-derived neurotrophic factor (BDNF) has key roles in neurodevelopment and synaptic plasticity and is implicated in affective disorders such as anxiety and depression. The aim of the present study was to use BDNF heterozygous mutant rats (HET) and wildtype controls (WT) to investigate the effect of BDNF downregulation on affective behaviours. We also assessed the longterm effects of young-adult stress, here simulated by chronic corticosterone (CORT) treatment. This treatment reduced anxiety-like behaviour in BDNF HET rats on the plus-maze but not in the open-field. There were no genotype or CORT effects on immobility time in the forced swim test. These results show differential effects of CORT treatment on anxiety-like behaviour in BDNF HET rats which were dependent on the experimental paradigms used. While these results do not negate the potential of BDNF HET rats in studies on the role of BDNF in affective disorders, caution is needed about experimental details and the choice of paradigms used.