Rat hypothalamic nuclei were removed and assayed for adrenocorticotropic hormone (ACTH), beta-endorphin (beta-END) and alpha-melanocyte-stimulating hormone (alpha-MSH) content by radioimmunoassay, from the same samples. We also performed immunostaining for these 3 pro-opiomelanocortin (POMC) derived peptides on paraffin embedded serial sections of the hypothalamus. Areas known to project to the external zone of the median eminence receive a dense POMC innervation while those projecting to the posterior pituitary are not innervated. In addition, hypothalamic areas previously suggested to project to medullary autonomic centers are densely innervated. This innervation pattern may provide the morphological basis for the involvement of POMC peptides in neuroendocrine and autonomic functions. The biochemical data raise the possibility that the POMC precursor is processed differently in various brain regions.