Brain-derived neurotrophic factor (BDNF) has been implicated as a molecular mediator of learning and memory. The BDNF gene contains four differentially regulated promoters that generate four distinct mRNA transcripts, each containing a unique noncoding 5[prime]-exon and a common 3[prime]-coding exon. This study describes novel evidence for the differential usage of alternative BDNF promoters and 5[prime]-exons during the consolidation of learning. We found a selective increase in BDNF transcripts containing exons I and III in the amygdala 2 h following fear conditioning, while mRNA levels of BDNF exons II and IV remained unchanged. These results provide the first evidence of differential splicing and/or differential BDNF promoter usage in response to a behaviorally relevant learning paradigm. (Contains 4 figures.)