AGO proteins are key players in RNA interference (RNAi) processes where they are guided by miRNA or siRNA to (partially) complementary sequences on mRNAs, resulting in target destabilization. In metazoans, cytoplasmic RNAi processes are well documented, but in recent years, evidence of nuclear RNAi has emerged to challenge our perspectives. Recently, we discovered nuclear RNAi in stem cells and showed that in the nucleus about half of miRNA binding sites are localized in introns and execute more potent gene silencing efficiency in the nucleus, as compared to the cytoplasm.