Cyclic nucleotide-gated (CNG) ion channels have been implicated as functioning in sensory transduction and in second-messenger modulation of synaptic neurotransmitter release. The olfactory, cAMP-sensitive CNG ion channel in vivo is considered to comprise the pore-forming CNG2 subunit together with CNG5 and CNG4.3 modulatory subunits. The expression of these 'olfactory' CNG subunit transcripts in microdissected subfractions of the rat cochlea and hair cell libraries has been investigated with RT-PCR. Unmodified transcripts of CNG2 were detected in the organ of Corti, lateral wall and spiral ganglion subfractions. CNG5 message was found in both the sensory organ of Corti and the non-sensory lateral wall subfractions but not in the spiral ganglion subfraction. The CNG5 sequence obtained for the organ of Corti fraction encompassed 78% of the olfactory CNG5 cDNA sequence. CNG5 message has also been detected in an inner hair cell cDNA library. In the lateral wall, unmodified CNG5 sequence was observed as well as truncated versions of CNG5 transcripts, one of which was also found in the rat brain. The truncated versions were characterized by deletions that resulted in a shift in reading frame and the premature appearance of a stop codon. The 'olfactory' CNG4.3 cDNA was amplified from all three subfractions. Within the cochlea, CNG2 immunoreactivity was selectively distributed in a pattern similar to that of adenylyl cyclase type I. Immunoreactivity to CNG2 has been localized to stereocilia of inner hair cells. CNG5 immunoreactivity was associated with stereocilia and lateral plasma membranes of outer hair cells. We conclude that transcripts necessary for a functional cAMP-sensitive CNG ion channel are present in the cochlea resulting from combinations of CNG2 with CNG5 and CNG4.3. Further, the localization of CNG2 and CNG5 immunoreactivity to hair cell stereocilia suggests a role for cAMP-sensitive CNG channels in hair cell signal transduction.