Solitary median maxillary central incisor syndrome is a rare disorder involving midline abnormalities such as holoprosencephaly, nasal cavity anomalies, cleft palate-lip, hypotelorism, microcephaly, and panhypopituitarism. Congenital nasal pyriform aperture stenosis is a lethal cause of neonatal respiratory distress due to narrowing of the pyriform aperture anteriorly and it can be confused with choanal atresia. In this report, we present a newborn infant with solitary median maxillary central incisor syndrome accompanied by other abnormalities including holoprosencephaly, nasal pyriform aperture stenosis, microcephaly and panhypopituitarism. Chromosomal analysis showed heterozygous SIX3 gene deletion at 2p21 region resulting in a more severe form of holoprosencephaly.