Recent studies indicate that hearing loss in humans has strong hereditary components associated with expression of specific genes in the auditory apparatus of the inner ear. However, the inner ear poses challenges for molecular research because the amount of tissue that can be isolated is limited, and extraction procedures yield small quantities of RNA and protein. To begin to identity genes essential for auditory function, we synthesized a cDNA library using an RT-PCR protocol and total RNA isolated from eight Xenopus laevis inner ears. Sequence analysis of randomly selected clones demonstrated expression of both identified (calmodulin, SNARE protein, syndecan-2) and unidentified genes, and confirmed synthesis of full length transcripts. Confocal and scanning electron microscopy (SEM) were used to examine the structure of inner ear organs that serve as auditory receptors in amphibians: the sacculus, the amphibian papilla and the basilar papilla. SEM images illustrate the heterogeneity of bundle morphology and demonstrate the continuous appearance of stereociliary bundles in the X. laevis amphibian papilla during larval development and adult life. Investigations of gene expression in Xenopus auditory organs using clones recovered from inner ear cDNA libraries should provide insight regarding the molecular basis of hearing.