Patients with X-linked lissencephaly with ambiguous genitalia (XLAG) syndrome present with lissencephaly, agenesis of the corpus callosum, refractory epilepsy of neonatal onset, microcephaly, and male genotype with ambiguous genitalia. The basis of the ambiguous genitalia in XLAG syndrome is not well-known. We report a case of the fourth child of healthy consanguineous parents who was presented to the hospital because of non-febrile seizures at 2 months of life. On physical examination, microcephaly, some dysmorphic face features, and ambiguous genitalia were determined. The cranial magnetic resonance imaging of the patient showed lissencephaly, agenesis of the corpus callosum, and enlarged ventricles. His karyotype was 46, XY. He had undetectable testosterone levels and elevated gonadotropins. Neither testicular tissue nor any testosterone response to human chorionic gonadotropin stimulation test was observed. These findings suggest that the hypogonadism in this patient with XLAG syndrome is primary hypogonadism due to gonadal agenesis or dysgenesis.