The establishment of the structure of the inner ear is under the influence of genes controlling complex networks of molecular interactions. Although several genes implicated in inner ear development have been identified in recent years (for review, see Torres and Giraldez 1998), the puzzle is still far from being assembled. Mouse mutants with behavioral abnormalities have been a great aid in the identification and isolation of a large number of genes expressed in the developing ear (Deol 1968, 1970, 1980; Steel 1995). However, in recent years, zebrafish (Danio rerio), an aquarium fish originating from the rivers of tropical India, has become a favorite animal model due to a rare combination of attractive features, including large progenies, external fertilization and embryonic development, embryo transparency, can obtain haploid and homozygous diploid individuals by gynogenesis (Streisinger et al. 1981, 1986; Streisinger 1984), and so on. A zebrafish genome-sequencing project has just begun at the Sanger Centre. Genetic linkage maps now cover the entire zebrafish genome (Knapik et al. 1998; Postlethwait et al. 1998; Gates et al. 1999; Shimoda et al. 1999). In addition, two independent physical maps made from zebrafish–rodent radiation hybrid lines (LN54 and T51) are available, which together cover >90% of the zebrafish genome (Geisler et al. 1999; Hukriede et al. 1999). Concomitantly, large-scale screenings for embryogenesis defects in zebrafish mutants have been carried out, which have permitted the identification of mutants with defects of the ear development. Twenty of these mutants, defining 13 independent loci, have been phenotypically and genetically characterized by Malicki et al. (1996). In an independent study, 95 mutants (39 genes) showing defects in inner ear development have been reported by Whitfield et al. (1996) among zebrafish mutants previously identified through a large-scale mutagenesis screening (Haffter et al. 1996). Another large-scale screening in zebrafish was announced by Amsterdam et al. (1999). The strategy of insertional mutagenesis proposed by this group is expected to accelerate the isolation of the disrupted genes. Despite some differences in the ear structure of otophysan compared to mammals (otophysan species, including zebrafish, have no middle or outer ear structure and they possess two sound-sensitive maculae in the inner ear instead of the mammalian organ of Corti), the hair cells, the sensory cells that detect sound waves and acceleration are remarkably conserved (Platt 1993; Popper and Fay 1993). The screening of zebrafish mutants for balance phenotypes combined with a candidate gene cloning approach is a potentially powerful strategy for revealing some of the genes that play a crucial role in the developing and functioning of hair cells. However, so far, only the myosin VIIA gene, which is defective in mariner zebrafish mutants, has been isolated (Ernest et al. 2000) on the basis of the involvement of its orthologs in balance defects and/or deafness in mice (Gibson et al. 1995) and humans (Weil et al. 1995). Improvement of the candidate gene approach requires a more extensive characterization of the genes expressed in the inner ear. This study is the first large-scale sequencing project aimed at gaining information on gene expression in the inner ear of developing zebrafish. The inner ear of zebrafish and other vertebrates differentiates from the otic placode, a dorso-lateral thickening of the surface ectoderm, adjacent to the rhombencephalon (Waterman and Bell 1984; Platt 1993; Haddon and Lewis 1996). In the zebrafish, the otic placode can be identified at 16 hr postfertilization (hpf). The placode gives rise to the otic vesicle (at 18 hpf), from which neuroblasts, the precursors of sensory neurons, will later delaminate to form the vestibuloacoustic ganglion. The peak of neuroblast delamination is between 22 and 30 hpf. At ∼24 hpf, the first hair cells differentiate within two sensory maculae. The three semicircular canals form between 43 and 72 hpf from the walls of the otocyst, and three additional clusters of hair cells soon become visible in the sensory cristae of these canals. Thus, by the end of the first week, all key structures of the ear are present, but before the ear is completely mature, thousands more hair cells and neurons will be produced by subsequent division of precursors (Waterman and Bell 1984; Haddon and Lewis 1996). Specifically, we focused this study on the 20–30 hpf stage, corresponding to the period of differentiation of the first hair cells and to the peak of neuroblast delamination (Waterman and Bell 1984; Haddon and Lewis 1996). The strategy of cDNA library subtraction was chosen because it has already been successful in identifying genes preferentially or specifically expressed in the human, mouse, and chicken auditory sensory organ (Robertson et al. 1994, 1998; Cohen-Salmon et al. 1997; Heller et al. 1998; Yasunaga et al. 1999; Simmler et al. 2000; Verpy et al. 2000, 2001). A pool of cDNAs from the liver was used as driver to minimize representation of housekeeping genes in the subtracted library.