Calcitonin gene-related peptide (CGRP), a well-known neuropeptide in primary sensory neurons carrying nociceptive information, includes two different peptides of similar structure, the α- and β-CGRP. The distribution of these two peptides in the central nervous system is known to be similar and no functional differences have been reported. The aim of this study is to investigated the changes of α- and β-CGRP expression following efferent or afferent disconnection of anterior horn cells in the rat spinal cord. One week after ventral rhizotomy (left L4-6), dorsal rhizotomy (left L4-6) or spinal cord transection (at lower thoracic level), the animals were sacrified and the L5 segments of the spinal cord were excised to perform immunohistochemistry and in situ hybridization histochemistry. In the control group, 4.45±1.51 anterior horn cells showed CGRP immunoreactivity per tissue section in one side. After ventral rhizotomy, the number of CGRP immunoreactive neurons increased to 9.12±2.52 at the ipsilateral ventral horn. After dorsal rhizotomy, CGRP immunoreactive neurons increased to 7.29±3.69 at the ipsilateral ventral horn and 6.26±1.53 at the contralateral ventral horn. In cases of spinal cord transection, almost all the anterior horn cells lost CGRP immunoreactivity in both sides. Neurons expressing α- or β-CGRP mRNA could be distinguished by in situ hybridization histochemistry. In the control group, anterior horn cells expressing α-CGRP mRNA numbered 4.16±1.32 per section and β-CGRP cells numbered 5.50±1.38. After ventral rhizotomy, the number of cells expressing α-CGRP mRNA increased to 10.07±2.86 in the ipsilateral side without any changes in β-CGRP mRNA expression. After dorsal rhizotomy, no significant changes in α-CGRP mRNA expression were detected, but the number of cells expressing β-CGRP mRNA increased to 7.45±2.04 in the ipsilateral side and to 7.02±1.38 in the contralateral side. In cases of spinal cord transection, the anterior horn cells lost α- and β-CGRP mRNA signals almost completely in both sides. These results showed that α-CGRP expression increased in axotomized anterior horn cells of the spinal cord, and that β-CGRP expression increased in anterior horn cells which had lost their afferent input through the primary sensory neurons. These findings provide evidence showing the functional difference of the two peptides in anterior horn cells of the spinal cord.