Stimulation of the nasal passages of muskrats with either ammonia vapours or retrogradely-flowing water produced cardiorespiratory responses (an immediate 62% decrease in heart rate, 29% increase in mean arterial blood pressure, and sustained expiratory apnoea). We used the immunohistological detection of Fos, the protein product of the c-fos gene, as a marker of neuronal activation to help elucidate the brainstem circuitry of this cardiorespiratory response. After repeated ammonia stimulation of the nasal passages, increased Fos expression was detected within the spinal trigeminal nucleus (ventral laminae I and II of the medullary dorsal horn, ventral paratrigeminal nucleus, and spinal trigeminal nucleus interpolaris), an area just ventromedial to the medullary dorsal horn, the caudal dorsal reticular formation and the area of the A5 catecholamine group compared to control animals. Repeated water stimulation of the nasal passages produced increased Fos expression only in the A5 catecholamine group. There was an increase in the number of Fos-positive cells in the ammonia group in the ventral laminae I and II of the medullary dorsal horn and the ventral paratrigeminal nuclei compared with the water group. We conclude that ammonia stimulation of the nasal passages produces a different pattern of neuronal activation within the brainstem compared with water stimulation. We also conclude that Fos immunohistochemistry is a good technique to determine functional afferent somatotopy, but that immunohistochemical detection of Fos is not a good technique to identify the medullary neurons responsible for the efferent aspects of an intermittently produced cardiorespiratory reflex.