ABSTRACT Cilia are nearly ubiquitous among eukaryotic cells and regulate important processes including motility, sensing, and signaling. In humans, both motile and immotile (primary) cilia are critical for development and homeostasis, with disruptions in ciliary function leading to a group of diseases known as ciliopathies. While the three- dimensional structure of the axoneme of motile cilia has been well-characterized, the molecular structures of primary cilia, as well as those that comprise the base of cilia (the basal body and transition zone) remain poorly understood. Taking aim at these gaps, I will use innovative approaches, including cryo-correlative light and electron microscopy, cryo-focused ion beam milling, cryo-electron tomography, and subtomogram averaging to generate high-resolution structures of primary cilia from mouse embryonic fibroblasts and the basal body/transition zone from Chlamydomonas cells. Furthermore, I will characterize the location, structure and molecular interactions of the transition zone protein Nephrocystin-4 (NPHP4), which helps regulate molecular trafficking into and out of the cilium and causes human ciliopathies when mutated. Specifically, I will visualize and compare ciliary structures from wild type and nphp4-null Chlamydomonas and precisely analyze the size and location of nphp4-mutant structural defects. This research will further our understanding of the three- dimensional architecture and function of cilia and reveal structural changes underlying ciliary disease mechanisms.