OBJECTIVE To study the mechanism of vestibular compensation and to observe the changes of c-Fos and NADPH-d expressions in the brainstem of the vestibular deafferentation rats in static status or following angular acceleration stimulation. METHODS Totally 60 SD rats were randomly divided into control group (labyrinthine intact), complete unilateral vestibular deafferentation (UVD) group, simultaneous complete bilateral vestibular deafferentation (BVD) group (n = 20 in each group). Subgroups (n = 10 in each subgroup) were set for static status or following angular acceleration stimulation in each group. Double labeling with histochemistry-immunohistochemistry was performed to observe c-Fos/NADPH-d neurons. RESULTS No positive c-Fos/NADPH-d expression was observed in the both sides of medial vestibular nucleus (MVN) and prepositus hypoglossi (PrH) of normal rats in static status and BVD rats whether following canal rotation or not. c-Fos/ NADPH-d expression was observed in the ipsilesional MVN and the contralesional PrH of UVD rats. However, c-Fos/NADPH-d were detected in both sides of MVN and PrH in UVD rats and normal rats following angular acceleration stimulation. CONCLUSION In the ipsilesional MVN and the contralesional PrH, c-Fos plays an important role in vestibular compensation, in which nitric oxide acts as a key neurotransmitter.