Long term functional impairments due to spinal cord injury (SCI) in the rat result from secondary apoptotic death regulated, in part, by SCI-induced decreases in protein levels of the anti-apoptotic protein Bcl-x L . We have shown that exogenous administration of Bcl-x L spares neurons 24h after SCI. However, long term effects of chronic application of Bcl-x L have not been characterized. To counteract SCI-induced decreases in Bcl-x L and resulting apoptosis, we used the TAT protein transduction domain fused to the Bcl-x L protein (Tat-Bcl-x L ), or its anti-apoptotic domain BH4 (Tat-BH4). We used intrathecal delivery of Tat-Bcl-x L , or Tat-BH4, into injured spinal cords for 24h or 7 days, and apoptosis, neuronal death and locomotor recovery were assessed up to 2 months after injury. Both, Tat-Bcl-x L and Tat-BH4, significantly decreased SCI-induced apoptosis in thoracic segments containing the site of injury (T10) at 24h or 7 days after SCI. However, the 7 day delivery of Tat-Bcl-x L , or Tat-BH4, also induced a significant impairment of locomotor recovery that lasted beyond the drug delivery time. We found that the 7 day administration of TatBcl-x L , or Tat-BH4, significantly increased non-apoptotic neuronal loss and robustly augmented microglia/macrophage activation. These results indicate that the anti-apoptotic treatment targeting Bcl-x L shifts neuronal apoptosis to necrosis, increases the inflammatory response and impairs locomotor recovery. Our results suggest that a combinatorial treatment consisting of anti-apoptotic and anti-inflammatory agents may be necessary to achieve tissue preservation and significant improvement in functional recovery after SCI.