Vesicle-associated membrane protein (VAMP; synaptobrevin) is involved in the molecular regulation of transmitter release at the presynaptic plasma membrane. VAMP exists in two isoforms, VAMP-1 and VAMP-2, which are transcribed from two separate genes and differentially expressed in the nervous system. In situ hybridization was used to examine whether VAMP isoform mRNA expression may be altered by experimental manipulations. The effect of nerve injury on VAMP-1 and VAMP-2 mRNA levels in motoneurones of the rat lumbar spinal cord was compared with lesion-induced changes in the expression of choline acetyl transferase (ChAT) and α-calcitonin gene-related peptide (α-CGRP) mRNA. After unilateral sciatic nerve transection (axotomy), VAMP-1 mRNA expression decreased significantly in parallel with a downregulation of ChAT mRNA in axotomized motoneurones compared with the corresponding motoneurones on the contralateral unlesioned side. There was a rapid decrease in VAMP-1 and ChAT mRNA levels at 2 days after axotomy, and at 7 days there was a 65% decrease in VAMP-1 mRNA and a 48% decrease in ChAT mRNA. VAMP-1 mRNA levels continued to decrease at 14 and 21 days, while ChAT mRNA levels had returned to normal at this time. In contrast, VAMP-2 and α-CGRP mRNA levels were upregulated in axotomized motoneurones. A significant increase for both VAMP-2 and α-CGRP mRNA levels was present 2 days after axotomy, and a maximum was reached after 7 days for α-CGRP mRNA (163%) and after 14 days for VAMP-2 mRNA (587%). Immunohistochemical analysis did not reveal any detectable changes in VAMP-1- or VAMP-2-like immunoreactivity in the motoneurone cell soma after axotomy. In the proximal end of the transected sciatic nerve, there was an increase in VAMP-1- and VAMP-2-LI, which was most prominent at 2 days after lesion. The results show that, in axotomized spinal motoneurones, VAMP-1 mRNA is downregulated and VAMP-2 mRNA is upregulated, indicating differential regulation of the two separate VAMP genes and differential roles for the two VAMP isoforms in the regulation of exocytosis after nerve injury.