The Trypanosoma brucei flagellum is vital for the organism's locomotion, pathogenesis and cell division. It contains a microtubular axoneme, a paraflagellar rod (PFR), and connecting proteins bridging these two structures. Our investigation by cryo-electron tomography revealed a characteristic arrangement of the axoneme internal features: the 9+2 arrangement of microtubule doublets displayed radial spoke spacing not found in other organisms. We have determined that the PFR is a quasi-crystal with a unit cell that repeats every 55 nm along the length of the axoneme. Connecting proteins are attached at 55 nm intervals (the spacing of a PFR repeat) along two of the nine doublets. During flagellar bending, the PFR unit cell axial lengths remain constant while the interaxial angles vary to accommodate the quasi-crystal's expansion and compression. RNAi silencing of one of the major PFR proteins completely abolished the assembly of the PFR, and resulted in defective cell motility. Our tomographic data of this mutated flagellum also showed that the microtubule doublets are not properly arranged within the axoneme. Thus the PFR simultaneously provides structural organization to the axoneme and the flexibility and regulation required for productive locomotion.Acknowledgements: This research has been supported by NIH grants (P41RR02250, training grant in molecular virology T32AI07471) and Singapore National Research Foundation Fellowship to CYH.