The structural basis for depressive disorders remains unknown. Studies using neuroimaging and postmortem brain tissue indicate that anatomic substrates may contribute to major depression disorder (MDD) and bipolar disorder (BD). The present study used design-based stereology to assess neuron loss in 2 well-defined hypothalamic structures, the paraventricular nucleus (PVN) and supraoptic nucleus (SON), in clinically well-studied cases with severe depression. The left or right diencephalon was blocked from 26 brains removed at autopsy from age-matched controls (5 male/3 female) and patients with MDD (6 male/5 female) and BD (5 male/2 female). Serial sections were cut at an instrument setting of 60 microm through the entire PVN and SON from left hypothalamus and 8 to 10 sections per brain were systematic-random sampled and stained with cresyl violet. A trained operator blind to clinical diagnosis used computerized stereology to estimate total neuron numbers in PVN and SON. The results revealed a selective, robust reduction of approximately 50% in total neuron number in the PVN for major depression and bipolar cases compared with age-matched controls, with no differences in neuron numbers in the SON. This selective neuronal loss in the PVN appears to identify an important neurobiologic substrate for the behavioral manifestations of depression.