The effect of cerium on mitochondria isolated from hybrid rice Shanyou 63 (Oryza sativa L) was investigated. Through in vivo culture, low dose Ce3+ promoted, but higher dose Ce3+, restrained mitochondrial heat production. However, through vitro incubation, Ce3+ showed only inhibitory action on mitochondrial energy turnover, the concentration required for 50% inhibition being 46.7 μM. In addition, Ce3+, like Ca2+, induced rice mitochondrial swelling and decreased membrane potential (△ψ), which was inhibited by the specific permeability transition inhibitor cyclosporine A (CsA). The induction approached a constant level while mitochondrial metabolism was fully prevented by Ce3+. These results demonstrated that cerium influenced rice mitochondria in vivo and in vitro via different action pathways, and the latter involved the opening of rice mitochondrial permeability.