Acute tryptophan depletion (ATD) is extensively used to investigate the implication of serotonin (5-hydroxytryptamine; 5-HT) in the onset and treatment of depression and cognitive disorders. Brain-derived neurotrophic factor (BDNF) is strongly linked to the 5-HT system and plays an essential role in mood and memory processes. The present study investigated the effects of ATD upon BDNF in serum, hippocampus and prefrontal cortex in the rat to further explore the underlying mechanism of ATD. ATD significantly decreased peripheral tryptophan (TRP) levels and moderately interrupted 5-HT metabolism 4h after administration of the nutritional mixture. Although no direct effects of ATD upon serum or brain BDNF concentrations were found, a stress-mediated, decrease in BDNF was observed in the prefrontal cortex. Moreover, brain TRP levels correlated positively with BDNF in both the prefrontal cortex and hippocampus. Thus, BDNF-mediated mechanisms due to ATD and/or its application stress might underlie ATD-induced neurochemical and behavioural alterations.