This study was performed to determine the three-dimensional (3D) structure of the murine temporal bone and to provide a survey atlas of the temporal bone structures in mice. The temporal bones of adult BALB/c mice were examined and 3D high-resolution reconstructions of the temporal bone were obtained using a micro-CT system. Using the system described here, the bony labyrinth and membranous labyrinth could be investigated in a non-destructive manner. The turning rate of the cochlea was two (human rate: two and a half). The shapes of the superior and posterior semicircular canals were more flexed than those in humans. The malleus manubrium was directed anteriorly and was thin and fan-shaped like a Persian sword. The size of the incus relative to the malleus was smaller than that in the human ossicles. The 3D reconstruction of murine temporal bone described in this study provides anatomical information that will be useful in future studies using mouse model.