We report chorea in an infant with holoprosencephaly. Congenital structural brain disease has not been a reported cause of chorea. Cranial magnetic resonance imaging revealed small, fused frontal lobes with hypoplastic caudates. Our patient responded to symptomatic treatment with dopamine-depleting agents. It is likely that the mechanism for the chorea was a dysfunction of the striatum. The differential diagnosis of childhood chorea should include holoprosencephaly.