The otic vesicle (otocyst) occupies a pivotal position in inner ear development, bridging the gap between otic placode determination, and morphogenesis of vestibular and auditory compartments. The molecular mechanisms underlying the progressive subdivision of the developing inner ear into different compartments, and the molecular control and execution of the different developmental processes involved, are largely unknown. Since relatively few genes have been implicated in these processes, we have undertaken this study to identify genes involved in these early embryonic stages. We have used cDNA subtractions of mouse otic vesicle against adult liver cDNA, and describe a set of 280 candidate genes. We have also performed otic vesicle RNA hybridizations against DNA chips to not only confirm the efficacy of the library approach, but also to investigate the utility of DNA array alternatives. To begin to dissect potential developmental roles, we investigated the spatial pattern of gene expression for a selected set of 80 genes in developing mouse embryos at mid-gestation by whole-mount in situ hybridization. These data illustrate the compartmentalisation of gene expression in the otic vesicle for the majority of genes tested, and furthermore, implicate many of the genes tested with distinct developmental subprocesses.