The septal nuclei are assumed to play a significant role in the pathophysiology of schizophrenia and affective disorders. The aim of this study was to morphometrically characterize the septal nuclei in patients with schizophrenia, bipolar disorder, and major depressive disorder, when compared with healthy control subjects. We analyzed the septal nuclei by determining the density and size of the neurons in postmortem brains in 17 patients with schizophrenia, 8 patients with bipolar disorder, 7 patients with major depressive disorder, and 14 control subjects matched for age and gender. There was a significant reduction in the neuronal density, but not in the mean cross-sectional area, in the lateral septal nucleus (P = 0.013) in patients with bipolar disorder when compared with control subjects. There were no significant changes in the neuronal density of the septal nuclei of the medial and lateral cell groups in patients with schizophrenia and major depressive disorder when compared with control subjects. There was a significant negative correlation between neuronal density in the lateral septal nucleus and disease duration in patients with major depressive disorder (P = 0.037, r = -0.9). The histopathological abnormality of the decreased neuronal density in the lateral septal nucleus, which is an important limbic region involved in emotions, might be a neuropathological correlate of bipolar disorder.