Cyclic AMP (cAMP)-dependent protein kinase (PKA) is a signalling molecule involved in the regulation of many physiological functions including those of cilia and flagella. PKA localizes to specific cellular structures and organelles by binding to AKAP (A-kinase anchoring protein) molecules via interaction with the regulatory subunits (RI and RII) of PKA. AKAPs are capable of forming multi-protein complexes to coordinate the action of several signalling molecules all at a single location. AKAPs also bind to a group of four proteins that share the RII dimerization/docking (R2D2) domain. R2D2 proteins are expressed at high levels in both the testis and spermatozoa and mutants lacking R2D2 proteins exhibit abnormal sperm motility. Thus AKAPs and AKAP associated proteins appear to be key molecules in the biochemical machinery regulating the functions of flagella and cilia.