The hypothalamus integrates physiological processes essential for survival and reproduction. Recent studies have shown that developmental events can affect these processes. Pathways required for the induction of the ventral midline of the hypothalamus or for the differentiation of specific hypothalamic lineages have the potential of causing endocrine and metabolic disorders, including obesity. Also, some genes with paternal monoallelic expression are involved in the development of hypothalamic centers that are critical physiological regulators. Developmental defects affecting the hypothalamus might represent a more frequent cause of clinical disorders than previously suspected.