The axonemal central pair (CP) are non-centrosomal microtubules critical for planar ciliary beat. How they form, however, is poorly understood. Here, we show that mammalian CP formation requires cooperative activities of Katanin, Camsaps, and Wdr47. Katanin severs peripheral microtubules to produce central microtubule seeds in nascent cilia. Camsaps stabilize minus ends of the seeds to facilitate MT outgrowth, whereas Wdr47 concentrates Camsaps into the axonemal central lumen to properly position the central microtubules. Wdr47 deficiency in mouse multicilia results in complete loss of CP, rotatory beat, and primary ciliary dyskinesia. Overexpression of Camsaps induces central microtubules in Wdr47-/- ependymal cells but at the expense of low efficiency, abnormal numbers, and wrong location, whereas overexpression of a dominant inhibitor of Katanin impairs the CP formation. We propose that Wdr47, Camsaps, and Katanin constitute a general cooperative work team for the generation of non-centrosomal MT arrays in polarized subcellular compartments.