Abstract A neonatal Dutch Warmblood colt was evaluated for inability to stand, incoordination and intention tremor. Despite partial improvement in clinical signs during the first 4 days of hospitalization, neurological deficits remained. Magnetic resonance imaging identified a unilateral infratentorial arachnoid cyst‐like lesion with ipsilateral compression and displacement of the cerebellar hemisphere, absent corpus collosum, polymicrogyria, suspect leukoencephalopathy, and noncompressive occipitoatlantal malformation. Improvement in clinical signs during the first 6 months of life suggests that horses can survive with complex congenital neurological malformations, but prognosis for athletic performance is poor. The accessibility of magnetic resonance imaging should improve the diagnostic accuracy of central nervous system disorders in neonatal foals in which congenital malformations are suspected. Euthanasia often is elected in foals with suspected congenital central nervous system disorders because of poor prognosis for athletic performance, limiting understanding of clinical progression in these cases.