In the present study, we use the anatomically well defined septohippocampal projection to study the molecular events involved in the reaction of neurons to axotomy. The expression of three immediate early genes (c-fos, c-jun, and jun B) was investigated in rat septohippocampal neurons after axotomy by bilateral fimbria-fornix transection (FFT). Moreover, the extent of retrograde degeneration in the septal complex was assessed by analyzing DNA fragmentation. In a postoperative time course analysis, a strong increase of c-jun immunoreactivity (IR) was observed in the nuclei of neurons in the medial septum/diagonal band complex (MSDB) 2 and 6 d postaxotomy, which was followed by a decline after 12 d and 3 weeks, respectively. Nine weeks after FFT, c-jun IR had disappeared. The c-jun-positive MS neurons were identified as former septohippocampal projection cells by double-labeling with the retrogradely transported tracer Fluoro-Gold injected into the hippocampus before axotomy. In line with the immunocytochemical data, there was a massive induction of c-jun mRNA in the axotomized MS neurons as visualized by in situ hybridization histochemistry. c-fos mRNA and c-fos or jun B IR were not detectable in either unoperated or lesioned medial septal neurons. Experiments using the TdT-mediated deoxyuridine triphosphate nick-end-labeling technique, designed to detect nuclear DNA fragmentation in degenerating neurons, complemented this study. During the postoperative time range studied, MS neurons did not exhibit DNA fragmentation. We conclude that MSDB neurons survive axotomy by FFT and display characteristic changes in gene expression.