Eukaryotic genomes are composed of individual genes and their intergenic regions. Traditionally, it has been held that the transcription of a gene always begins from the transcription start site and ends at the termination site, the gene is referred as an individual transcription unit. However, some sporadic studies indicate that transcription can sometimes read-through the intergenic region and generates a large fusion transcript which contains the upstream gene, intergenic region and the downstream adjacent gene. The fusion transcript becomes a mature functional transcript after intergenic splicing. The patterns of intergenic splicing, possible generation mechanism and its significance are summarized.