The discovery of RNA interference (RNAi) has opened new avenues in biology and medicine. In addition to post-transcriptional gene silencing, new findings are expanding the range of action of small duplex RNAs and broadening the spectrum of the potential applications of RNAi-based therapeutics. In recent years a complex and heterogeneous network of non-protein coding RNAs (ncRNAs) with potential regulatory functions has come into the spotlight providing an unexpected perspective on the mechanisms of transcriptional and epigenetic control of gene expression in human cells. The spread and complexity of these RNA-based transcriptional regulatory networks are still to be explored. However, they are likely to be important mechanisms controlling gene expression in human cells. As we will learn more about these processes, endogenous small RNAs and ncRNAs participating in these transcriptional regulatory networks might become valuable targets to modulate expression of genes involved in human diseases. Thus, understanding these basic processes of gene regulation might be translated in the near future into innovative therapeutic strategies to treat human diseases.