[Purpose] The purpose of this study was to examine the effects on stroke patients of trunk stabilization exercise on different support surfaces. [Subjects and Methods] Sixteen stroke patients with onset of stroke six months earlier or longer were randomly and equally assigned to group I (exercise performed on a stable support surface) and group II (exercise performed on an unstable support surface). The two groups conducted the trunk stabilization exercises on the respective support surfaces, in addition to existing rehabilitation exercises five times per week for 12 weeks. Changes in the cross-sectional area (CSA) of the muscles were examined using computed tomography (CT), and changes in the balance ability were assessed using a measuring system and the trunk impairment scale (TIS). [Results] In group I, there was a significant increase in the CSA of the mulifidus muscle on the side contralateral to the brain lesion and in the paravertebral and multifidus muscles on the side ipsilateral to the brain lesion. In group II, there was a significant increase in the CSA of the paravertebral and multifidus muscles on the side contralateral to the brain lesion and on the side ipsilateral to the brain lesion. In terms of changes in balance ability, the sway path (SP) and TIS significantly improved in group I, and the SP, sway area (SA), and TIS significantly improved in group II . [Conclusion] Exercise on the unstable support surface enhanced the size of the cross-sectional area of the trunk muscles and balance ability significantly more than exercise on the stable support surface.