The eukaryotic phylum apicomplexa encompasses many thousands of parasite species of medical and veterinary importance, including Plasmodium sp. and Toxoplasma gondii. These obligate intracellular parasites survive and replicate within suitable eukaryotic hosts, ultimately rupturing infected cells to release parasites that can invade neighboring cells. Repeated cycles of infection and lysis are responsible for the pathogenesis associated with these parasites. Apicomplexan parasites replicate using an unusual process known as endodyogeny or schizogony, in which daughters are constructed de novo within the mother. This distinctive mode of replication relies on dynamic assembly of an organelle known as the Inner Membrane Complex (IMC): a patchwork of flattened vesicles (alveoli) intimately associated with cytoskeletal proteins. The IMC is highly dynamic, and its assembly, disassembly and localization within the parasite are critical for many important functions, including parasite motility, maintenance of structural integrity, and partitioning maternal organelles among progeny parasites. Most studies on the IMC have focused on its cytoskeletal components; little has been known about the assembly of this organelle's membrane components. This dissertation investigates the biogenesis and fate of the IMC, using Toxoplasma as a model system. Exploiting an IMC integral membrane protein as a marker (GAP40), live cell imaging of fluorescent protein reporters, photobleaching and photoactivation techniques, has permitted us to define IMC morphology and dynamics throughout the replicative cycle of T.gondii. This work demonstrates that initial assembly and elongation of the T.gondii IMC involves de novo synthesis, but following emergence from the mother cell, the daughter IMC continues to grow via recycling of the maternal IMC. As a series of flattened membrane vesicles, the IMC appears to arise from the Golgi apparatus, via vesicular trafficking machinery. We have therefore examined SNARE proteins potentially involved in the biogenesis of the IMC. Genome wide analysis and phylogenetic reconstruction permitted classification of apicomplexan putative SNAREs (25 In T. gondii, 24 in P. falciparum). Functional predictions based on SNARE motif and subcellular localization reveals conservation of SNAREs involved in the early secretory pathway, highlighting the stripped-down apicomplexan endomembrane system, and providing a map of SNAREs likely to be involved in distinctive parasite function(s).