Defects in the primary cilium – which extends from the surface of most eukaryotic cells – can lead to several disorders, but little is known about how individual ciliary proteins function or how they are compartmentalised. For instance, mice that lack the cilium-localised protein inversin (Inv) have situs inversus (mirror-image rearrangement of the visceral organs) and develop multiple renal cysts, but have no apparent defects in ciliary structure. On page 44, Takahiko Yokoyama and colleagues use immuno-EM and confocal microscopy to explore the subciliary distribution of Inv. The authors first show that Inv-GFP and endogenous Inv localise to a region near the base of the cilium that is distinct from previously identified subciliary compartments – they term this region the Inv compartment. Next, they use truncated Inv-GFP constructs to identify a ninein-homologous sequence at the C-terminus of Inv that is essential for its localisation to the Inv compartment. Notably, mutations in this region – which is distinct from the Inv cilium-targeting sequence – have been associated with kidney disease in humans. Finally, the authors use FRAP to show that Inv is dynamic within the Inv compartment. They conclude that the Inv compartment is a novel region within the primary cilium that might be required to maintain normal renal architecture.