In experimental models of spinal cord trauma there is often a relatively poor correlation between light microscopic histological changes and motor recovery. Previously it was shown that spinal cord levels of immunoreactive TRH and substance P, by radioimmunoassay, are significantly reduced caudal to the injury site. Since much of the substance P and TRH in the spinal cord derives from cells within the ventral medulla, many of which also contain serotonin, we examined changes in serotonin immunoreactivity within the spinal cord caudal to the injury site in rats subjected to varying degrees of impact trauma to the thoracic cord. Reductions in immunocytochemical staining of serotonin in ventral gray matter of the lumbar region at two weeks after trauma were significantly correlated with the degree of injury severity as reflected by motor impairment. Changes in the region of the central canal, but not dorsal horn, were also correlated with injury severity. These findings indicate that serotonin immunocytochemical analysis may permit better correlation between anatomical and functional outcome after spinal cord injury than generally utilized light microscopic methods.