Basal bodies are modified centrioles that give rise to cilia and flagella. The basal body is a complex structure that can form through at least two distinct pathways depending on the cell type. Corresponding to this structural complexity, the basal body proteome contains a large number of proteins, many of which correspond to cilia-related disease genes, especially genes involved in nephronophthisis and cone-rod dystrophy. Basal bodies appear to play several roles in the cell. First, they provide a ninefold symmetric template on which the ninefold symmetry axonemal structure of the cilium can be built. Second, they dictate the position and orientation of the cilium, which is especially critical for ensuring that cilia-driven fluid flows move in the correct direction. Third, they are the point at which entry of proteins into the cilium is regulated. Finally, recent evidence suggests that basal body position may be involved in coupling planar cell polarity cues with the axis of cell division. Defects in any of these functions could lead to disease symptoms. Current studies of basal body biology include both proteomic and genetic approaches, relying on ciliated cell culture lines as well as genetically tractable systems such as Chlamydomonas reinhardtii. The "parts list" of basal body proteins and genes is rapidly being completed, opening the way to more mechanistic studies in the future.