In order to detect whether there were different expression patterns of Fos protein induced by somatic or visceral noxious stimulation in the serotonergic neurons in the rat brainstem, an immunohistochemical double-labelling technique for serotonin (5-HT) and Fos was employed after subcutaneous or stomach injection of formalin. The two stimuli were matched in pilot experiments to produce maximum Fos expression. The expression of Fos protein in 5-HT-containing neurons (5-HT/Fos co-localized neurons) could be observed in the ventrolateral subdivision of the midbrain periaqueductal grey, interpeduncular nucleus, paramedian raphe nucleus, all of the brainstem raphe nuclei, the alpha part of the gigantocellular reticular nucleus and the lateral paragigantocellular reticular nucleus. The locations of the 5-HT/Fos co-localized neurons in the brainstem of animals subjected to somatic noxious stimulation were similar to those subjected to visceral noxious stimulation. However, the number and proportion of the 5-HT/Fos co-localized neurons in the median raphe nucleus and nucleus raphe obscurus of the rat subjected to visceral noxious stimulation were statistically greater than those in rats subjected to somatic noxious stimulation. These results suggest that serotonergic neurons in median raphe nucleus and nucleus raphe obscurus have a tendency to higher neuronal activity after visceral noxious stimulation.