The anatomic concept of the hypothalamus changed considerably since its earliest definition. Tridimensional reconstructions, experiments and many staining methods have expanded considerably the number of anatomical details recognized in this territory, probably one of the most complex in the brain. For a long time the predominant anatomic view has interpreted the hypothalamus as a longitudinal column at the floor of the diencephalon, connected rostrally with the telencephalon and caudally with the midbrain. However, recent advances in our knowledge of early developmental mechanisms seem increasingly contradictory with this columnar viewpoint. Consideration of early ventralization, dorsalization and anteroposterior patterning effects suggests that, rather than being a diencephalic floor element, the hypothalamus is best understood as a transverse region lying ventral to the telencephalon and rostral to the diencephalon; the latter separates it from the midbrain.