Skin pain differs from muscle pain in quality and affective dimension, but it is unknown how the brain processes the nociceptive inputs from skin and muscle differently. To delineate the differential effects of nociceptive inputs from skin and muscle, the EEG topography and power spectra were analysed on the basis of two databases acquired from two separate studies regarding skin (Neurosci. Lett. 305 (2001b) 49) and muscle pain (Exp. Brain Res. 141 (2001c) 195). The same experimental protocol was applied to the same subject-group in the two separate experiments. In the two independent experiments, skin pain and muscle pain were, respectively, induced by intracutaneous and intramuscular injection of capsaicin in the left forearm. Visual analogue scale (VAS) and EEG data acquired before, during the vehicle and capsaicin injections were quantitatively compared. The results showed that the VAS profiles for skin and muscle pain are highly similar in spite of distinct qualities perceived. Skin pain produced a similar but not identical EEG topographic pattern as muscle evoked. Muscle pain induced a significant increase of beta-2 activity in the extensive frontal, parietal and occipital areas compared to skin pain. No difference was found between the vehicle-induced non-painful sensations in skin and muscle. These results implicate that the nociceptive inputs from muscle and skin are processed differently in the similar neural matrix of the brain.