Immunocytochemistry with an antiserum directed against serotonin (5-HT) was used to assess the development of the representation of the body surface in the rat's primary somatosensory cortex (S-I). Within 1 hour of birth (P-O), 5-HT-positive fibers were present in the marginal zone, the cortical plate, and developing layers V and VI. Immunoreactivity in the marginal zone consisted of a thin band of coarse fibers oriented parallel to the pia. Only a small number of isolated fibers were visible in the cortical plate. A denser network of both coarse and fine fibers could be seen in presumptive layers V and VI. By the first hour of P-I, 5-HT-positive axons in the deeper cortical plate were organized into a crude representation of the rat's body surface. At this age, aggregates of fibers corresponding to the head, lower jaw, trunk, and forepaw could be clearly distinguished. These regions of dense 5-HT immunoreactivity consisted primarily of fine caliber axons that had invaded the lower part of the cortical plate. Dense aggregates of fine caliber axons were also visible in developing layers V and VI. Coarse 5-HT-positive fibers were visible in all layers, but they did not appear to contribute to the pattern that corresponded to the body surface. By the first hour of P-2, the map of the body surface in S-I was more refined and a row-related organization of 5-HT-immunoreactive fibers was visible in the portion of the cortex representing the vibrissa pad. The laminar distributions of coarse and fine caliber serotoninergic axons at this age were essentially the same as on P-I. By P-2.5 (60 hours after birth), patches of 5-HT-positive fibers corresponding to individual vibrissa follicles were clearly evident. These consisted of dense aggregates of fine caliber axons that were centered in presumptive layer IV, but which also extended above and below this lamina. Over the next 3 days, the pattern continued to mature. By P-4, dense 5-HT labelling was also visible in the secondary somatosensory cortex (S-II). By the beginning of P-5, clusters of fibers corresponding to more rostral facial hairs and individual digits within the forepaw representation could also be discerned. By P-12, the differential distribution of 5-HT fibers in S-I was no longer visible. Thus, immunocytochemistry for serotonin showed a representation in S-I homeomorphic with the body surface prior to the age at which it can be discerned with other methods thought to reveal thalamocortical axons. Transection of the infraorbital nerve (ION) on the day of birth altered the organization of the vibrissal representation in the contralateral cortex from the earliest age at which it could be detected by 5-HT immunocytochemistry in normal animals. However, the departure from the normal organization was gradual. Row-related organization was clearly visible in the cortices of rats sacrificed on P-3, but not in those of rats that were killed on P-5. These results suggested that the organization of the 5-HT innervation of the cortex may be guided by thalamic afferents and further that some aspects of this guidance persist, albeit temporarily, after ION transection on P-0. The 5-HT immunoreactivity that we observed in the developing somatosensory cortex was not contained in thalamocortical axons. Unilateral electrocautery of the ventrobasal thalamus on P-4 did not reduce the density or alter the pattern of the 5-HT innervation of the cortex in rats that were examined on P-6.