In the developing brain, mature brain derived neurotrophic factor (mBDNF) and its precursor (proBDNF) exhibit prosurvival and proapoptotic functions, respectively. However, it is still unknown whether mBDNF or proBDNF is a major form of neurotrophin expressed in the immature brain, as well as if the level of active caspase-3 correlates with the levels of BDNF forms during normal brain development. Here we found that both proBDNF and mBDNF were expressed abundantly in the rat brainstem, hippocampus and cerebellum between embryonic day 20 and postnatal day 8. The levels of mature neurotrophin as well as mBDNF to proBDNF ratios negatively correlated with the expression of active caspase-3 across brain regions. The immature cortex was the only structure, in which proBDNF was the major product of bdnf gene, especially in the cortical layers 2-3. And only in the cortex, the expression of BDNF precursor positively correlated with the levels of active caspase-3. These findings suggest that proBDNF alone may play an important role in the regulation of naturally occurring cell death during cortical development.