The pedunculopontine nucleus (PPN), which is located in the upper brainstem, contains cholinergic and non-cholinergic neurons, and has afferent and efferent connections to the basal ganglia and spinal cord. The PPN is known to be affected in adult-onset basal ganglia diseases, and we speculated that the PPN might be similarly insulted in developmental basal ganglia disorders. We immunohistochemically examined the expression patterns of acetylcholine esterase and tyrosine hydroxylase, markers of acetylcholinergic and catecholaminergic neurons, respectively, in the PPN pars dissipata (PPNd) of controls and patients with bilirubin encephalopathy (BE) and perinatal hypoxic ischemic encephalopathy with localized basal ganglia lesion (HIEbg). Controls showed an age-dependent change in the percentages of acetylcholinergic and catecholaminergic neurons. Three out of six BE cases and three out of six HIEbg cases showed a reduction in the percentage of acetylcholinergic neurons in the PPNd. Additionally, three BE cases demonstrated an increase in the percentage of catecholaminergic neurons. It is likely that the relative proportions of acetylcholinergic and catecholaminergic neurons in the PPN can be altered in developmental basal ganglia disorders.