We have analyzed the regulation of brain-derived neurotrophic factor (BDNF) mRNA expression in the nigrostriatal system following neurotoxin ablation of striatal targets by means of kainate (KA) or quinolinic acid (QA) injections. Loss of nigral target cells in the striatum was accompanied by significant induction of BDNF mRNA levels in the ipsilateral substantia nigra (SN) at 12 and 24 h post lesion. Dual tyrosine hydroxylase (TH) and BDNF mRNA in situ hybridization (ISH) confirmed the dopaminergic nature of the BDNF mRNA expressing cells. Analysis of neuronal activity in terms of cFos mRNA expression demonstrated intense induction of this marker in the ipsilateral SN pars reticulata (SNPR), but not in SN pars compacta. Dual glutamic acid decarboxylase (GAD) and cFos mRNA ISH confirmed this view. Colchicine injections into the medial forebrain bundle to specifically disrupt neuronal trafficking between SN and striatum induced BDNF mRNA levels in the ipsilateral SNPC, thus demonstrating that nigral expression of BDNF mRNA is dependent of striatal target tissue. In addition, we found significant elevations of BDNF in the subthalamic nucleus following striatal excitotoxic lesion, which may bring novel roles of BDNF in the basal ganglia complex.