Objective To investigate the effect of recombinant botulinum neurotoxin serotype A heavy chain (BoNT/ A heavy chain) on local proteins which are related to nerve growth after spinal cord injury in rats, and to get some experimental evidence to explain the mechanism of BoNT/ A heavy chain in stimulating neuritogenesis. Methods Recombinant botulinum neurotoxin serotype A heavy chain was applied locally or intrathecally to rats with ipsilateral semidissociated lumbar spinal injury. Local spinal tissue was extracted for general protein expression by two dimension electrophoresis plus nitrate silver staining after different time period of injury. Based on the results of 2-D gelelectrophoresis, growth-associated protein 43 (GAP-43) and of superior cervical ganglion 10 (SCG 10) were selected to examine the changes of their expression and distribution features under BoNT/ A heavy chain administration using SDS-PAGE, western blot and immunofluorescence. Results (1) The model of spinal cord injury (SCI) in this study was an ipsilateral semi?dissociated lumbar SCI in rat. The rats showed obvious motor and sensory dysfunction in the ipsilateral hind limb. (2) The results from 2-D gel electrophoresis plus nitrate silver staining showed that the administration of BoNT/ A heavy chain based on SCI altered the local protein expression pattern. The decrease or increase in the expression of some protein dots / dots group was clearly seen after single SCI. However, these changes were transformed by BoNT/ A heavy chain treatment, which appeared as a reversed pattern turning toward that in control group or further increased expression upon SCI, such as the dots located respectively at 35 -45 kDa and 18 -25 kDa level, pI between 5 -7. In addition, the expression of the two dots located at the level as above increased after SCI only, and showed further increase in their expression with BoNT/ A heavy chain intervention. (3) The changes of selective GAP-43 and SCG 10 expression and distribution by western blot and immunofluorescence indicated that the administration of BONT/ A heavy chain based on SCI amplified the expression of GAP-43 and SCG 10 (P < 0.05). Meanwhile, the positive immuonfluorescent staining for both GAP-43 and SCG 10 mainly distributed nearby the proximal area of injury, both cytoplasm and neuronal processes were positively stained. Conclusions Intrathecal delivery of BoNT/ A heavy chain increases the expression of growth-associated proteins GAP 43 and SCG 10 after SCI in rats.