Eukaryotic cells utilize vesicular trafficking pathways to transport various proteins and lipids between their organelles. These trafficking pathways are regulated in part via small GTPases. There are two conserved GTPases required for early secretory pathway function: Sar1 and Rab1. The activated, GTP-bound, form of Sar1 recruits the cytoplasmic COPII vesicle coat machinery to the ER membrane in the first stage of the eukaryotic secretory pathway. Active Rab1 recruits tethering factors and other effectors to promote the transport and fusion of COPII vesicles. Understanding the mechanisms involved in activation of these small GTPases is critical for our comprehension of vesicular trafficking. Here, I describe my investigations into the structure and function of the GEFs (guanine nucleotide exchange factors) involved in activating both Sar1 and Rab1. Activation of Sar1 at the ER by Sec12, a membrane-anchored GEF, is the initiating step of the secretory pathway. I solved the structure of a complex between Sar1 and the cytoplasmic GEF domain of Sec12. This structure represents the key nucleotide-free activation intermediate and reveals how the K-loop of Sec12 disrupts the nucleotide binding site of Sar1. I also propose a mechanism for how Sec12 facilitates membrane insertion of the amphipathic helix exposed by Sar1 upon GTP-binding, based on an unexpected basic patch on the GEF domain. Rab1 is activated by the TRAPPIII complex (transport protein particle) in both Golgi trafficking and in autophagy. I determined the molecular structure of the TRAPPIII complex bound to the nucleotide-free Rab1 intermediate and propose a mechanism for its orientation at the membrane surface. I also describe our efforts to unify the apparently discordant observations of TRAPP complexes in budding yeast and mammalian cells. There have been four distinct TRAPP complexes described in budding yeast and only two in mammalian cells. This difference has prevented a clear understanding of the specific functions of TRAPP complexes in all cell types. We demonstrate that as in mammalian cells, budding yeast have only two TRAPP complexes, TRAPPII and TRAPPIII. Our findings lead to a simple yet comprehensive model for TRAPPIII function in all eukaryotic cells.