Recent brain imaging studies have been revealing central processing of muscle pain. However, there is hardly a consensus on a brain region specifically responsible for muscle pain, not for skin pain. To seek out this specific region, we used event-related functional magnetic resonance imaging (MRI) and the 3-T MRI scanner. Twelve healthy male subjects participated in this study. Electric stimulation with 1-ms duration was applied to two sites: the left anterior tibial muscle and the skin just above it. The stimuli consist of three levels in strength both for skin and muscle stimulation, i.e. nonpainful, painful (5/10 in visual analog scale, VAS) and more painful (7/10 in VAS). Group analysis revealed that brain regions activated by muscle stimulation included ipsilateral superior frontal gyrus, postcentral gyrus (primary somatosensory cortex, SI), posterior cingulate; contralateral precentral gyrus, medium dorsal nucleus (thalamus), superior temporal gyrus; bilateral middle frontal gyrus, cingulate gyrus and lenticular nuclei. These regions are similar to those reported by other researchers and some of them are known to be activated during pain. Brain regions specifically activated by muscle stimulation, not by skin stimulation, were ipsilateral culmen, cingulate gyrus; contralateral lenticular nucleus, pons, paracentral lobule (SI), substantia negra, medial frontal cortex and bilateral middle temporal gyrus. These regions may play an essential role to distinguish muscle pain from skin pain in the brain. [J Physiol Sci. 2006;56 Suppl:S89]