In the present study we compare the formation of vibrissa-related patterns by thalamocortical afferents from the ventrobasal (VB) nucleus to that by raphe-cortical, serotonergic afferents from the raphe nuclei. In opposite hemispheres of the same brain, 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (Dil) labeling of VB afferents and serotonin (5-HT) immunohistochemistry reveal that the pattern of vibrissa-specific patches is first exhibited by thalamocortical axons in barrel field cortex. Shortly thereafter, 5-HT axons form patches in the same locations as the dense concentrations of VB afferents. To assess a possible role of 5-HT afferents in the specification of barrel field cortex, neonatal rat pups were administered p-chloroamphetamine (PCA), a selective 5-HT neurotoxin. The formation of vibrissa-related patterns by thalamocortical and serotonergic afferents was compared in normal and PCA-treated rat pups at various developmental stages. PCA treatment led to a significant decrease in the number of serotonergic axons in barrel field cortex. Despite this decrease, VB afferents segregated in patches over individual barrels. However, a delay in the emergence of the thalamocortical pattern was noted in toxin-treated animals. We conclude that PCA treatment does not prevent formation of a vibrissa-specific pattern by thalamocortical afferents, and discuss the possibility that the 5-HT axons may play a trophic role in the maturation of VB afferents.