The ciliary transition zone (TZ) is a complex structure at the base of the cilium/flagellum where the basal body meets the plasma membrane. In Drosophila spermatids, the transition zone is located at the base of the ciliary cap, separating the compartmentalized axoneme tip and the cytosolic axoneme. The TZ plays a structural and functional role by regulating the traffic in and out of the cilium and by forming structural links between microtubules and the membrane. (Adapted from FBrf0233737 and FBrf0233580).