The hypothalamus is one of the most complex region in the central nervous system regarding neuroanatomy, neurochemical content, neuropeptide/classical neurotransmitter interactions, physiological actions, and pathophysiology. Hypothalamic neuropeptides have been involved in a large plethora of mechanisms related with obesity, anxiety, feeding, energy metabolism, defensive behavior, mood, and reproduction. The therapeutic potential of these findings is enormous but the physiological complexity occurring in the hypothalamus is huge due in part to the interactions between numerous neuropeptides as well as between neuropeptides and other neuroactive substances. Here, we review the development and neuroanatomy of the hypothalamus as well as the involvement of 31 neuropeptides in hypothalamic functions and pathologies. Alterations in the secretion, release, and/or concentrations of neuropeptides and/or their hypothalamic receptors can trigger different pathologies. Several therapeutic strategies that could be carried out by adjusting neuropeptide levels in the hypothalamus are suggested. The combination of imaging techniques with a detailed neurochemical knowledge of the hypothalamus would be an excellent diagnostic tool, allowing personalized treatment. Several approaches for future research that may contribute to improve or resolve these pathologies are also mentioned.