Basic and clinical research is revealing that various noncoding and small RNAs play important and diverse roles in germ cell development and quality, including X/Y silencing during meiosis, gene regulation, DNA damage responses, and protection of the genome against transposable elements. Indeed, mammalian germ cells are known to harbor multiple small RNA species, including small interfering RNAs (siRNA), microRNAs (miRNA), and germline-specific PlWI-interacting RNAs (piRNA). However, their mechanistic roles in gametogenesis and human infertility are largely uncharacterized. The Cornell Center for Reproductive Genomics (CRG), established in 2006, has developed emerging strengths in the area of small RNA biology to address these gaps in our understanding. The goal of these studies is to elucidate the role of small RNA pathways in the events that give rise to viable euploid gametes. Four projects are proposed: Project I (PI: Andrew Crimson) will define the temporal profile of small RNA expression and small RNA targets throughout spermatogenesis, focusing on the onset of, and progression through, prophase I in the mouse; Project II (PI: Darius Paduch) will explore the roles and expression of microRNAs in human male germ cell and somatic compartments, and will examine changes in the profiles of testicular small RNAs In infertile men; Project III (PI: Paula Cohen) will explore the role of the Argonaute family of small RNA binding proteins in the critical process of meiotic silencing during prophase I in mice. Three cores are proposed: an Administrative core, and Outreach Core and an RNA sequencing core, the latter being open to all SCCPIR members. Collectively, these studies represent the most comprehensive analysis of small RNA pathways in mammalian gametogenesis to date, and will provide a cutting-edge program in small RNA regulatory processes that will be a unique and timely addition to the SCCPIR network. The combined focus on comparative analysis of small RNA pathways in the germline is likely to contribute greatly to the understanding of how these pathways may function to ensure the production of healthy gametes.