Holoprosencephaly (HPE) is caused by the impaired cleavage of the embryonic prosencephalon, and in the severest type, alobar HPE, the normally bilateral diencephalon and basal ganglia are fused and tend to incorporate into the upper brainstem. The detailed neuropathological features of HPE remain to be elucidated, although disturbed regulation in body temperature and electrolyte balance are frequently observed. We immunohistologically examined the expression of hypothalamic hormones, neurotransmitters, calcium-binding proteins and neuropeptides in six female autopsy cases of alobar HPE. Eight age-matched controls formed the comparative basis for the immunoreactivity of these markers during the fetal period. Neurons immunoreactive for either vasopressin or orexin-A were noted in the fused diencephalon in five HPE cases, and colocalization of vasopressin and tyrosine hydroxylase occurred in HPE cases surviving more than 6 months. Tyrosine hydroxylase-immunoreactive fibers and neurons were observed in the fused diencephalon and basal ganglia in all the six cases. Parvalbumin-immunoreactive structures were identified in the fused diencephalon and basal ganglia in five cases, and the apparent red nucleus was identified by anti-parvalbumin immunostaining in two cases aged more than 1 year. Five cases demonstrated substance P-immunoreactive structures in the diencephalon, and a substantia nigra-like structure in the midbrain was visualized by immunostainings for both tyrosine hydroxylase and substance P in four cases. Only two cases aged more than 1 year had immunoreactivity for methionine-enkephalin in the basal ganglia and substantia nigra. These data suggest that the fused diencephalon and basal ganglia exhibited functional developments in alobar HPE, and the disturbed expression of the markers may be involved in hypothalamic and/or motor abnormalities in patients.