Pain includes a negative affective component, although the neural system is unclear. The amygdala including the lateral (La), basolateral (BL) and central (Ce) nuclei is thought to play a key role in emotional responses. In this study, we analyzed the c-fos mRNA expression, as a marker of neuronal activity, induced by two types of pain, chemical somatic and visceral noxious stimuli, in each amygdaloid nucleus in unanesthetized rats. We found that intraplantar injection of formalin as a chemical somatic noxious stimulus increased c-fos mRNA expression in the La and BL, but not Ce. On the other hand, intraperitoneal injection of acetic acid as a chemical visceral noxious stimulus induced it highly in the Ce, moderately in La and hardly in BL. These results suggest that distinct amygdaloid nuclei are activated by chemical somatic and visceral noxious stimuli, which might differentially contribute to emotional responses by them.