Although several approaches to stimulate axonal regeneration after spinal cord injury have succeeded in stimulating robust growth of axons into a lesion site, the growth is generally highly disorganized, losing the distinct arrangement of axonal tracts within the spinal cord. Previously described freeze-dried agarose scaffolds, composed of individual, uniaxial channels extending through their entire length, were prepared with and without recombinant Brain-Derived Neurotrophic Factor (BDNF) protein and tested in an adult rat model of spinal cord injury to determine whether regenerating axons could be guided across a site of injury in an organized fashion. After 1 month, both the cellular and axonal responses within and around scaffolds were evaluated. Scaffolds were found to be well integrated with host tissue, individual channels were penetrated by cells, and axons grew through scaffolds in a strikingly linear fashion. Furthermore, the regeneration was significantly augmented by the incorporation of BDNF protein into the walls and lumen of the scaffold. These findings clearly demonstrate that axonal regeneration can be organized and guided across a site of injury.