Cilia are hair-like organelles extending from the cell surface that execute motile (e.g. respiratory cilia) and/or sensory functions (e.g. renal monocilia). The basic ultrastructure of cilia and flagella has been well established by electron microscopy. Several recent reports have now provided intriguing new insights into the complex molecular composition of cilia and flagella. These data from genome, proteome and transcriptome analyses will facilitate the systematic discovery and understanding of genes responsible for human cilia-related diseases, such as primary ciliary dyskinesia, polycystic kidney disease and male sterility.