We presented a case of an asymmetric phenotype of Axenfeld-Rieger anomaly in one eye and aniridia in another of a patient with a novel nonsense point mutation of PITX2. The current case undermines the variability in phenotype even between the two eyes of an individual affected by ARS and the advantage of genetic testing in correctly diagnosing a rare disease. Here, PITX2 is linked to Axenfeld-Rieger syndrome.