High-throughput analysis of RNA molecules in multicellular eukaryotes has revealed an abundance of complementary antisense RNAs that are transcribed from separate or overlapping genes. In mammals these include many novel non-coding RNAs of unknown function. This unexpected complexity of the mammalian transcriptome suggests that expression of many genes is regulated post-transcriptionally by mechanisms mediated by RNA-RNA base pairing. The recent discovery of the widespread expression of microRNAs in animals and plants provides a prototypic example of such regulation in eukaryotes. However, there are likely to be numerous other types of antisense regulation in eukaryotes, many as yet uncharacterized.