To search for genes that could be involved in genetic disorders primarily involving the retina and the cochlea, we tried to identify mRNAs preferentially expressed in retina and cochlea and to establish their chromosomal localization. Two approaches were employed. First, a mouse subtracted library (retina + cochlea against liver + brain) was generated. Randomly selected cDNA clones were sequenced and compared to databases. Tissue expression of some of them was analyzed by RT-PCR. Using radiation hybrid cell lines, the mouse chromosomal localization was determined for those showing the highest level in the retina and the cochlea. Second, human Expressed Sequence Tags (ESTs) with preferential expression in the retina and the cochlea were searched for in databases, and chromosomal localization was also established. From 171 sequenced clones, 73 were classified as known genes (with 17 clones coding for 6 genes), 86 were homologous to ESTs, and 12 were unidentified. Of 108 selected clones, 22 (18.5%) had the highest level of expression in the retina and/or the cochlea, while expression was higher in another tissue or ubiquitous for 60 (55.5%) and 22 (20.4%) of them, respectively. By RT-PCR, one clone similar to the mouse Asic3 cDNA (proton-gated channel) was found mainly in the retina and cochlea, but its human ortholog was widely expressed. We selected 17 ESTs from the UniGene database with restricted expression including in the retina and cochlea. We mapped 10 of these ESTs as well as four mouse clones from the subtracted library. Some of them localized to morbid intervals. The combined information from expression analysis and chromosomal localization allowed for the identification of potential candidate genes for retinal diseases (CORD8, CORD9) and syndromic blindness/deafness/renal defects.