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Waltzing guinea pigs are an inbred guinea pig strain with a congenital and progressive balance and hearing disorder. A unique rod-shaped structure is found in the type I vestibular hair cells, that traverses the cell in an axial direction, extending towards the basement membrane. The present study estimates the total number of utricular hair cells and supporting cells in waltzing guinea pigs and age-matched control animals using the optical fractionator method. Animals were divided into four age groups (1, 7, 49 and 343 day-old). The number of type I hair cells decreased by 20% in the 343 day-old waltzing guinea pigs compared to age-matched controls and younger animals. Two-photon confocal laser scanning microscopy using antibodies against fimbrin and βIII-tubulin showed that the rods were exclusive to type I hair cells. There was no significant change in the length of the filament rods with age. Taken together, our data show that despite rod formation in the type I hair cells and deformation of hair bundles being present at birth, the type I hair cell population is not affected quantitatively until a year after birth.