Choline acetyltransferase of the peripheral type (pChAT) is a splice variant that lacks exons 6–9 of the common-type ChAT (cChAT); the role of pChAT remains unknown. We investigated the expression of pChAT and cChAT after axotomy to try to elucidate its function. In the dorsal motor nucleus of the vagus nerve (DMNV), nucleus ambiguus (NA), and hypoglossal nucleus (HN) of control rats, we observed neural expression of cChAT but no pChAT-positive neurons. Following nerve transection, we clearly detected pChAT-labeled neurons in the DMNV and weakly labeled neurons in the NA, but pChAT was not seen in the HN. In the DMNV, the mean number of cChAT-positive neurons decreased rapidly to 40.5% of control at 3 days post transection, and to 5.0% of control after 7 days. The number of cChAT-positive neurons then gradually increased and reached a plateau of about 25% of control value at 28 days post transection. pChAT-positive neurons did not appear until 7 days after transection. On the same day, pChAT mRNA was detected in the DMNV neurons by reverse transcription-polymerase chain reaction (RT-PCR) by using laser capture microdissection. The number of pChAT-positive neurons gradually decreased, and only 10% of the cholinergic neurons retained pChAT expression 56 days post transection. Double-immunofluorescence analysis showed that some of the DMNV neurons expressed both cChAT and pChAT upon recovery from axotomy. These results suggest that the expression of pChAT is associated with the regenerative or degenerative processes of motoneurons especially for general visceral efferents. J. Comp. Neurol. 513:237–248, 2009. © 2009 Wiley-Liss, Inc.