Objective To investigate the different patterns of cochlear hair cell loss in CBA/ CaJ and C57BL/6J mice with aging. Methods Thirty-two CBA/ CaJ or C57BL/6J mice at 6, 12, 18, and 24 months of age were selected, with 8 mice in each age group. The cochleae were removed under general anesthesia, and then the intact basement membrane was taken out from the cochlea and used for making glass slides of whole cochlear basement membrane. The numbers of cochlear inner and outer hair cells were counted, and input into the computer using cochleogram software. The density of cochlear hair cells in the two mouse strains were compared at corresponding ages, and statistically analyzed. Results The outer hair cells from cochlear apex in the CBA/ CaJ mice at 12 months of age began to loss slightly. With the increase of age, the losses of outer hair cells were continuously expanded, and their developments were mainly from the top to the middle part. The losses of inner hair cells also occurred in the later period. From 18 months of age on, the losses of the cochlear outer hair cells were increased significantly by comparison with that of the last age ( P < 0. 05). However, the losses of the outer and inner hair cells at the cochlear bottom appeared in C57BL/6J mice at the 6 months of age, and the losses were mainly of the outer hair cells. From then on, the losses of outer hair cells were continuously expanded with the increase of age. From 6 months of age on, the losses of the cochlear outer and inner hair cells were increased significantly compared with that of the CBA/ CaJ mice at the same age ( P < 0. 05). From 12 months of age on, the losses of the cochlear outer and inner hair cells were increased significantly compared with that of the same strain( P <0. 05). Conclusions The damages of cochlear hair cells in the CBA/ CaJ mice obey the rule of pathological changes that began at both ends of the cochlear top and bottom, and extended to the middle part, but the damages of hair cells at cochlear top were more serious than that at the cochlear bottom. The damages of cochlear hair cells in the C57BL/6J mice obey the rule of pathological changes that began mainly at the cochlear bottom and gradually extended to the middle and top. The damages of outer hair cells are earlier than that of inner hair cells. The damages of hair cells in C57BL/6J mice are earlier than that in CBA/ CaJ mice. These result suggest that both species of mice can be used as animal models for the research of age-related hair cell apoptosis, but the model of C57BL/6J mouse is more suitable for the research of short-term observation. The differences of hair cell changes between the CBA/ CaJ and the C57BL/6J mice may be related to the mutation and deletion of Cdh23 gene.