Recent studies have shown that endogenous small RNAs regulate a variety of biological processes during vertebrate development; however, little is known about the role of small RNAs in regulating developmental signaling pathways during early embryogenesis. In this study, we applied Illumina sequencing to characterize an unexpected endogenous small RNA catalog and demonstrated a dramatic transition from transposon-derived piRNA-like small RNAs (pilRNAs) to microRNAs (miRNAs) in pre- and post-gastrula chicken embryos. The comprehensive expression profile of chicken miRNAs at the pre- and post-gastrula stages revealed that most known and new miRNAs were dynamically regulated during development. In addition to embryonic stem cell-related miRNAs, Gene Ontology (GO) analysis showed that miRNAs enriched in early stage chicken embryos targeted multiple signal transduction pathways associated with the reproductive process and embryogenesis, including Wnt and TGF-β, which specifies the neural fate of blastodermal cells. Intriguingly, a large cohort of pilRNAs primarily derived from the active and most abundant transposable elements (TEs) were enriched in chicken stage X blastoderms. Within stage X blastoderms, pilRNAs were specifically localized to the primordial germ cells (PGCs), indicating their post-zygotic origin. Together, these findings imply a role for small RNAs in gastrulation in early stage chicken embryos.