The spinal cord is richly innervated by serotoninergic fibres originating from the raphe nuclei. The localization of the terminating component of serotoninergic neurotransmission, the serotonin transporter SERT1, was found in both the dorsal and ventral horns, especially at the level of the cervical and lumbar segments. Within the thoracic region, we observed a heavily labelled bundle in the intermediolateral nucleus of lamina VII. A low density of stained fibres was encountered in the sacral spinal cord. In contrast to homogeneous staining of motor nuclei, a differential labelling of laminae was seen in the dorsal horn, with laminae I, III and IV exhibiting a higher density of immunopositive terminals than the medial part of lamina II. High magnification revealed a preferential accumulation of serotonin transporter staining within nerve endings and varicosities of thin fibres. Double immunofluorescence staining demonstrated a co-localization of serotonin and its uptake system within these varicosities. These results show that the serotonin transporter is highly expressed in the rat spinal cord and that its distribution parallels the serotoninergic innervation. They also reinforce the view that varicosities are important neuronal structures, which modulate the function of dorsal and ventral horn neurons by releasing serotonin.