Vestibular compensation, the neuronal process underlying behavioral recovery from vestibular dysfunction produced by unilateral labyrinthectomy, is attributed to functional reorganization of neuronal circuits in the brainstem and cerebellum. Climbing fibers originating from the inferior olive are suggested to play a crucial role in this compensatory process. To assess the possible contribution of brain-derived neurotrophic factor (BDNF) to the function of climbing fibers during vestibular compensation, we investigated the BDNF mRNA expression in the rat inferior olive after unilateral labyrinthectomy by quantitative in situ hybridization. We found several induction patterns depending on the subregions of the inferior olive 6 h after unilateral labyrinthectomy. First, in the dorsal cap and the ventrolateral outgrowth, the expression levels increased on the side contralateral to the lesion and decreased on the ipsilateral side. Second, in the beta nucleus, C subnucleus of the medial accessory olive, and A/B subnuclei of the medial accessory olive, we detected an increase in the mRNA expression level on the side contralateral to the lesion, but no changes in the expression level on the ipsilateral side. In the beta nucleus, where the strongest induction was observed, the mRNA expression level increased nearly five-fold. Third, in the dorsomedial cell column, the mRNA expression levels increased on both sides. Finally, we did not detect significant changes in mRNA expression levels in the other subregions of the inferior olive, the dorsal accessory olive, principal olive and rostral medial accessory olive. The changes in BDNF mRNA expression reverted to control levels by 72 h after the labyrinthectomy. The inferior olive subregions that showed changes in BDNF mRNA expression levels send climbing fibers to the cerebellar cortical regions that, in turn, project to the vestibular nuclei. Therefore, BDNF induced in these subregions could contribute to the functional reorganization of the olivo-cerebellar system for vestibular control.