The hallmark of stem cells is their ability to self-renew meanwhile capable of producing numerous differentiated daughter cells. Previously, we identified the ARGONUATE/PIWI protein family to be essential for stem cell self-renewal in diverse organisms. This protein family can be divided into ARGONUATE and PIWI subfamilies. Recently, we and others discovered that the PIWI subfamily proteins interact with a novel class of non-coding small RNAs that we named PIWI-interacting RNAs (piRNAs) (Lin H, Science, 2007). There are at least 60 000 species of piRNAs. They are mostly 26∼32 nucleotides in length, and are abundantly expressed during spermatogenesis. Individual piRNAs frequently correspond to intergenic and repetitive sequences. In addition, a small number of piRNAs correspond to exonic and intronic sequences. This broad genomic distribution of piRNAs implicates their potential involvement in diverse mechanisms of gene regulation during spermatogenesis. Our latest work suggests that PIWI subfamily proteins and specific piRNAs are involved in epigenetic programming as well as the regulation of mRNA stability and, possibly, translation. Such regulations are involved in controlling the self-renewing division of germline stem cells and other gametogenic events in Drosophila and mammals.