Kainic acid induces excitotoxicity and nerve cell degeneration in vulnerable regions of rat brain, most markedly in hippocampus and amygdala. Part of the cell death following kainic acid is apoptotic as shown by caspase 3 activation and chromatin condensation. Here we have studied the regulation of pro‐ and anti‐apoptotic proteins belonging to the Bcl‐2 family in rat hippocampus and amygdala by kainic acid in relationship to ensuing neuronal death. The pro‐apoptotic protein Bax was up‐regulated in hippocampus 6 h after kainic acid administration. The increase in Bax was followed by the appearance of TdT‐mediated dUTP nick end labelling‐positive cells which were prominent at 24 h. Immunohistochemistry for active Bax revealed a punctated labelling of neurons in the CA3 and hilar regions of hippocampus as well as in amygdala. Double staining for NeuN, a marker for nerve cells, and TdT‐mediated dUTP nick end labelling showed that mainly neurons undergo degeneration after kainic acid treatment. In contrast to Bax, the pro‐apoptotic BH3‐only Bcl‐2 proteins Bim and Harakiri/DP5 were down‐regulated by kainic acid. This was also observed for the anti‐apoptotic proteins Bcl‐x and Bcl‐w. Immunoreactive Bcl‐2 was up‐regulated in hippocampus after kainic acid together with an increase in the phosphorylation of serine‐87 in Bcl‐2, suggesting a post‐transcriptional modification of the protein. This was confirmed using immunoprecipitation of total Bcl‐2 from hippocampus and amygdala which revealed an increase in serine‐87 phospho‐Bcl‐2 after kainic acid. Inhibition of the c‐jun N‐terminal protein kinase pathway reduced both serine‐87 phosphorylation and cell death after kainic acid. This indicates an important role of Bcl‐2 phosphorylation in controlling neuronal death after kainic acid. In contrast to the situation in trophic factor‐deprived neurons, no up‐regulation of Bim or Harakiri/DP5 proteins occurred after kainic acid, suggesting alternative pathways for regulation of cell death in excitotoxicity. The results indicate that not only the relative levels of Bcl‐2 family proteins but also conformation changes and post‐translational modifications contribute to neuronal death following kainic acid.