Borna disease virus (BDV) is a nonsegmented, negative-strand RNA virus that causes neurologic disorders in a wide range of animal species. Although the virus is unclassified, sequence analysis of the 8.9-kb viral genome has shown that it is related to rhabdoviruses and paramyxoviruses. We have mapped subgenomic RNAs of BDV strain He80-1 to the viral genome by determining the precise sequences at their 5' and 3' termini. This analysis showed that the genome contains three transcription initiation sites and four termination sites. A 14- to 16-nucleotide semiconserved sequence was present at the gene start sites and partially copied into the subgenomic RNAs. The termination sites contained a U-rich motif reminiscent of termination signals in rhabdoviruses and paramyxoviruses. In contrast to the genomes of other nonsegmented, negative-strand RNA viruses, the BDV genome lacked the typical configuration of termination signal, intergenic region, and initiation signal at the gene boundaries. Instead, transcription units and transcription signals frequently overlapped. These differences have implications for our understanding of the control of viral transcription and may relate to the low-level replication and persistence of BDV.