AbstractCilia, the hair-like protrusions that beat at high frequencies to propel a cell or move fluid around the cell, are composed of radially bundled doublet microtubules. The doublet microtubule is composed of a 13-protofilament A-tubule, a partial 10-protofilament B-tubule and microtubule inner proteins (MIPs) inside the tubulin lattice. In this study, we present the near-atomic resolution map of theTetrahymenadoublet microtubules. The map demonstrates that the network of microtubule inner proteins is weaving into the tubulin lattice, forming an inner sheath of proteins. In addition, we also obtain the tubulin lattice structure with missing MIPs by Sarkosyl treatment. In this structure, the tubulin lattice showed significant longitudinal compaction and lateral angle changes between protofilaments. These results are evidence that the binding of MIPs directly affects and stabilizes the tubulin lattice. It is also suggested that the doublet microtubule is an intrinsically stressed filament and this stress could be exploited in the regulation of ciliary waveforms.