Semicircular canals are sensory organs for balance, consisting of fluid-filled tubules that are arranged perpendicularly to each other in inner ear. The precise mechanism of the morphogenesis of this unique organ is still under investigation. Semicircular canals arise from the flattened pouch of epithelium. The centers of two apposing wall of the pouch approach each other and form a fusion plate. The clearing of the fusion plate makes a hole and leaves the remaining tissue as semicircular canals. Three mechanisms have been proposed for this clearing: programmed cell death, epithelial-mesenchymal transition, and retraction of the cells in the fusion plate to surrounding semicircular canals. Previous studies have revealed programmed cell death in the fusion plate, although other two hypotheses were not disproved. Here we examined the contribution of epithelial-mesenchymal transition and epithelial retraction to the morphogenesis of semicircular canals. We analyzed immunohistochemically the structural change in the epithelium of the developing fusion plate using molecular markers, basal lamina component laminin, cytoskeletal F-actin, and cellular junctional marker β-catenin. Our observation revealed that fusion plate epithelium lost its apico-basal polarity and intermingled with facing fusion plate cells, associated with the disruption of basal lamina. Moreover, there were several cells with mesenchymal appearance adjacent to the torn basal lamina. We also found the merging of apposing basal laminae at the border between forming canal and breaking fusion plate. These observations suggest that the epithelial-mesenchymal transition, rather than the epithelial retraction, may be responsible for clearing fusion plate cells.