Gene silencing via the RNA interference (RNAi) pathway is an evolutionary conserved process that is critical for the control of gene expression in organisms ranging from yeast to humans. Targets of RNAi are recognized through complementary base-pairing interactions with small RNAs that act as guides to RNAi effector complexes. Several distinct classes of endogenous small RNAs, including microRNAs, endo-siRNAs and piRNAs, regulate gene expression states to impact diverse biological processes. Our lab focuses on understanding the nature and biological functions of small RNA pathways in animals. We have identified and characterized an evolutionary conserved small RNA pathway that operates in germ cells and that is critical both for germline stem cell maintenance and for gametogenesis. Working in Drosophila and mice, we discovered a new class of small RNAs, Piwi-interacting (pi)RNAs. Piwi/piRNA pathway plays an important role in genome integrity by repressing selfish repetitive elements. A characterization of piRNA sequences in combination with genetic studies revealed that the biogenesis and function of piRNAs differs from that of other classes of small RNAs. While canonical small RNAs, such as microRNAs, affect gene expression post-transcriptionally, our studies suggest that piRNAs most likely serve as guides for de novo DNA methylation in mouse male germ cells.