Neurological cases, especially in foals, are rare in the daily practical work. The most common causes are traumata and infectious diseases of the central nervous system (CNS). This case report provides further insights into the wide spectrum of possible neuropathological lesions by detailing a complex malformation with unilateral neurological signs that occurred later post natum. Thus, clinicians should also be aware of malformations in case of respective neurological patients. A Hanoverian foal was presented with progressive ataxia. General and blood examination revealed no further alterations. By neurologic examination, a unilateral hypermetria was diagnosed and a cysternography of the head was performed. A cerebellar malformation was assumed and the foal was euthanized due to poor prognosis. At necropsy, a unilateral absence of a cerebellar hemisphere and vermis accompanied by contralateral malformation of the mesencephalon was diagnosed. The missing areas of the right cerebellar hemisphere were replaced by a cystic formation. The left part of the mesencephalic lamina quadrigemina was reduced in size and the corpus callosum was hypoplastic. Additional microscopical findings were most obvious near the cyst formation and included angiofibrosis in remaining cerebellar and mesencephalic parenchyma and leptomeninges, heterotopia of cerebellar neurons, sclerosis in cerebellar cortex, focal proliferation of meningeal cells and mild mononuclear perivascular infiltrates. Occassional irregular neuronal arrangement in the mesencephalon was also present. Infectious agents such as Borna disease virus, rabies virus, and equine herpesvirus were not detected. Therefore, the complex malformation in this foal might have been caused by a destructive, possibly ischemic event, or could represent a sequel of a primary retrocerebellar cyst with accompanying compression of adjacent parenchyma.