At the post-transcriptional level, gene expression is largely regulated through a network of molecular machines that regulate pre-mRNA maturation integrity, transport, translation and degradation. These processes are based on the formation of nucleoprotein complexes and require the recognition of sequence motifs on the RNA. By masking these targets with complementary RNA sequences forming Watson-Crick base pairing, it is possible to efficiently and specifically impact on the cell phenotype, or to compensate the deleterious effect of mutations. Here we review how the adeno-associated virus technology is being exploited for expressing non-coding RNAs in tissues such as the brain, muscle or liver, in functional genomic studies as well as for the development of novel therapeutic strategies.