Septins are a family of highly conserved small GTPases that heterooligomerise and assemble into filaments, rings or spirals. Septins regulate cytokinesis and, during interphase, they localise to actin stress fibres and also to microtubules; the latter localisation is negatively controlled through the interaction between septins and the microtubule-associated protein MAP4. It has recently been shown that septins form a ring structure at the base of the primary cilium and that septin 2 (SEPT2) is involved in ciliogenesis, but the underlying mechanisms are unknown. Alexandre Benmerah and co-workers now (p. 2583) set out to further characterise these septin functions by analysing their distribution in human-telomerase-immortalised human retinal pigmented epithelial (RPE) cells, which are widely used models for studying ciliogenesis, as well as in tissues. Using a proteomic approach, they find that SEPT2 forms an equimolar complex with SEPT7 and SEPT9 that localises along the entire length of the axoneme of cilia. This complex positively controls ciliogenesis and the length of cilia, and, consistently, ablation of any of these septins by RNA interference inhibits ciliogenesis, as shown previously for kidney epithelial cells. Furthermore, the authors demonstrate that MAP4 also localises to the axoneme where it antagonises the function of the SEPT2–SEPT7–SEPT9 complex by controlling its access to microtubules and, therefore, exerts a negative effect on cilia length.