In molecular biology, an axoneme, also called an axial filament, is the microtubule-based cytoskeletal structure that forms the core of a cilium or flagellum.

The axoneme serves as the "skeleton" of these organelles, both giving support to the structure and, in some cases, the ability to bend.

Thought to be important in regulating the motion of the axoneme, this "T"-shape complex projects from each set of outer doublets toward the central microtubules.

Axonemal doublet microtubules assemble from the ends of nine centriolar/basal body triplet microtubules, whose ninefold symmetry and clockwise pinwheel pattern (looking from inside the cell to the flagellar tip) is organized by the conserved protein of the SAS6 gene, and which is introduced into some eggs to establish the first mitotic spindle.

Currently, the molecular structure of the axoneme is known to an extraordinary resolution of <4 nm through the use of cryo-electron tomography, as initially pioneered by Nicastro.

These ciliopathies include polycystic kidney disease (PKD), retinitis pigmentosa, Bardet–Biedl syndrome, and other developmental defects.