A previous three-dimensional reconstruction of the rat hypothalamus revealed an organization of nuclei into three major clusters. This clustering may relate to the presence of three hypothalamic anlagen in the embryo and to a restriction of marker proteins and transcription factors to specific regions of the hypothalamus during development. To see if a similar clustering was apparent in the human hypothalamus, a reconstruction of the hypothalamus from a male cadaver was prepared. The reconstruction showed a clustering of nuclei into three anterior-posterior groups. With reference to the well-defined human supraoptic nucleus, the suprachiasmatic and lateral mammillary nuclei were proportionately smaller in this single human specimen than would be expected from data in the rat. A high degree of homology between hypothalamic structures in the rat and human were generally observed.