Although the gross embryology of inner ear development has been documented for several different vertebrate species at a descriptive level, our understanding of the molecular mechanisms involved remains rudimentary. Therefore, we have used cDNA subtraction and normalization procedures to define genes upregulated in the 13.5dpc mouse inner ear, a developmental stage where inner ear morphogenesis and tissue remodeling is active and differentiation of future hair cells is being initiated. We recovered 33 different genes from this subtraction and using gene-specific primers have confirmed the transcriptional upregulation of 26 of these in the 13.5dpc inner ear. Northern analyses were used to investigate splicing differences between the inner ear and the whole embryo at 13.5dpc. Spatial localization of expression was determined through whole-ear in situ hybridization analysis, and selected genes were analyzed in more detail through in situ hybridization of tissue sections. These data illustrate that the genes isolated in this study are expressed in the developing otic capsule and/or neuroepithelium. Furthermore, the expression patterns also reveal molecular heterogeneity in the developing capsule and indicate that for some genes, the chondrogenic otic capsule is composed of distinct domains of gene expression.