Morteza Seifi and colleagues report a novel deletion involving the coding region of PITX2 in a small kindred with Axenfeld-Rieger syndrome (ARS). The minimum size of the deletion is 1 421 914 bp that spans one upstream regulatory element (CE4), PITX2 and a minimum of 13 neighbouring genes. The maximum size of the deletion is 3 789 983 bp. They report also an other novel deletion is a 2-bp deletion in a non-coding exon of the remaining PITX2 allele predicted to alter correct splicing. This is the first study reporting on bi-allelic changes of PITX2 potentially contributing to a more severe ARS phenotype.