Loss of cilia and ciliary protein causes various abnormalities (called 
ciliopathy), including situs inversus, renal cystic diseases, polydactyly and 
dysgenesis of the nervous system. Renal cystic diseases are the most frequently 
observed symptoms in ciliopathies. Cilia are microtubule-based organelles with 
the following regions: a ciliary tip, shaft, transitional zone and basal 
body/mother centriole. Joubert syndrome (JBTS), Meckel Gruber syndrome (MKS) and 
Nephronophthisis (NPHP) are overlapping syndromes. Recent studies show that JBST 
and MKS responsible gene products are localized in the transitional zone of the 
cilia, where they function as a diffusion barrier, and control protein sorting 
and ciliary membrane composition. Nephrocystins are gene products of NPHP 
responsible genes, and at least 11 genes have been identified. Although some 
nephrocystins interact with JBST and MKS proteins, proteomic analysis suggests 
that they do not form a single complex. Localization analysis reveals that 
nephrocystins can be divided into two groups. Group I nephrocystins are 
localized in the transitional zone, whereas group II nephrocystins are localized 
in the Inv compartment. Homologs of group I nephrocystins, but not group II 
nephrocystins, have been reported in C. reinhardtii and C. elegans. In this 
review, we summarize the structure of the ciliary base of C. reinhardtii, C. 
elegans and mammalian primary cilia, and discuss function of nephrocystins. We 
also propose a new classification of nephrocystins.