X-linked lissencephaly with ambiguous genitalia is a rare and recently described syndrome. We report a neonate presenting with the classical features of the syndrome which includes lissencephaly, agenesis of the corpus callosum, intractable epilepsy of neonatal onset, acquired microcephaly, and male genotype with ambiguous genitalia. The baby was managed aggressively with antiepileptics. Early clinical suspicion of the syndrome can prevent future such occurrences in the family through genetic counseling.