Small non-coding RNAs comprise several classes and sizes, but all share a unifying function in cellular physiology: epigenetic regulation of gene expression. Here, we review the salient aspects of recent studies on the biogenesis and function of three classes of small RNAs: miRNAs, siRNAs, and piRNAs. Although the mechanisms are becoming clear by which siRNA-triggered mRNA cleavage silences genes, more studies are needed on several issues regarding miRNA-mediated translation repression. Piwi proteins have been suggested to co-operate in amplifying piRNA biogenesis to maintain transposon silencing in the germ line genome, but details of this process are still unknown as well as the functional consequences of piRNA expression at discrete genomic loci.