To investigate the molecular basis for the poor regenerative capacity of the mammalian central nervous system (CNS) after injury, we searched for genes whose expression was affected by an adult rat spinal cord hemi-section. Differential screening of a rat spinal cord expression library was performed using polyclonal antibodies raised against lesioned spinal cord tissue. A striking overexpression was found for ahnak, encoding a 700-kDa protein, in normal CNS present only in the blood–brain barrier (BBB) forming vascular endothelial cells. Indeed, very early after spinal cord injury (SCI), high levels of membrane-associated AHNAK are observed on non-neuronal cells invading the lesion site. With time, AHNAK distribution spreads rostrally and caudally concomitant with the process of tissue inflammation and axon degeneration, delineating the interior surface of cystic cavities, mainly in front of barrier-forming astrocytes. Strong overexpression is also observed on vascular endothelial cells reacting to BBB breakdown. Based on our detailed analysis of its spatiotemporal and cellular expression, and its previously described function in BBB, we suggest that AHNAK expression is associated with cell types displaying tissue–protective barrier properties. Our study may thus contribute to the elucidation of the precise molecular and cellular events that eventually render traumatic spinal cord tissue non-permissive for regeneration.