Exon trapping is a molecular biology technique to identify potential exons in a fragment of eucaryote DNA of unknown intron-exon structure. This is done to determine if the fragment is part of an expressed gene.

The genomic fragment is inserted into the intron of a 'splicing vector' consisting of a known exon - intron - exon sequence of DNA. If the fragment does not contain exons (i.e., consists solely of intron DNA), it will be spliced out together with the vector's original intron. On the other hand, if exons are contained, they will be part of the mature mRNA after transcription (with all intron material removed). The presence of 'trapped exons' can be detected by an increase in size of the mRNA.