We report a complete 3D structural model of typical epithelial primary cilia based on structural maps of full-length primary cilia obtained by serial section electron tomography. Our data demonstrate the architecture of primary cilia differs extensively from the commonly acknowledged 9+0 paradigm. The axoneme structure is relatively stable but gradually evolves from base to tip with a decreasing number of microtubule complexes (MtCs) and a reducing diameter. The axonemal MtCs are cross-linked by previously unrecognized fibrous protein networks. Such an architecture explains why primary cilia can elastically withstand liquid flow for mechanosensing. The nine axonemal MtCs in a cilium are found to differ significantly in length indicating intraflagellar transport processes in primary cilia may be more complicated than that reported for motile cilia. The 3D maps of microtubule doublet-singlet transitions generally display longitudinal gaps at the inner junction between the A-and B-tubules, which indicates the inner junction protein is a major player in doublet-singlet transitions. In addition, vesicles releasing from kidney primary cilia were observed in the structural maps, supporting that ciliary vesicles budding may serve as ectosomes for cell-cell communication.primary cilium | 3D structure | electron microscopy E pithelial primary cilia are hair-like, membrane-enveloped cellular projections that extend into the extracellular space. They are sensors detecting environmental signals for modulation of cellular physiological activities. Due to the importance of these cellular activities, defects in primary cilium assembly/disassembly (ciliogenesis) and maintenance underlie many developmental and organ disorders (1-3). Accurate information of the 3D structure of primary cilia is essential to fully understand the process and regulation of primary ciliogenesis.In mammalian organs, such as kidney, liver, and pancreas, each epithelial cell carries a single primary cilium as a mechanosensor, which bends reversibly under liquid flow (4-6). The passive elastic bending of primary cilia is believed to modulate epithelial cell proliferation and autophagy, thereby maintaining the normal architecture of mature organ tissues essential to their physiological functions, although the identity of the signaling messenger is controversial (2, 7-13). The elastic bending property relies on the structure of the ciliary microtubule-based framework (axoneme). The 3D architecture of primary cilium axoneme is fundamental to understanding the mechanosensory function of primary cilia in kidney and other cells.Electron microscopic (EM) studies of both primary cilia and motile cilia started over half century ago (14-18). The primary cilium axoneme has long been described as a "9+0" architecture, with 9 peripheral microtubule doublets of the same length forming a hollow cylindric architecture as the core framework based on some electron micrographs (1,(17)(18)(19)(20)(21)(22)(23)(24). The 9+0 model is currently the most accepted structural underst...