Mutations in the PAX6 gene mostly cause non-syndromic aniridia with autosomal dominant inheritance and familial occurrence. The underlying point mutations and deletions in the PAX6 locus cause loss-of-function of one gene copy (haploinsufficiency). Mutations with residual PAX6 function often result in milder disease expression but may also cause distinct and more severe ocular phenotypes. Combined deletion of PAX6 and the adjacent WT1 tumor suppressor gene causes Wilms tumor, aniridia, genitourinary anomalies and mental retardation (WAGR) syndrome with a high risk for Wilms tumors in infancy.Genetic diagnostics are important for confirming the clinical diagnosis, for the assessment of the risk of recurrence and early recognition of children with associated tumor risk.Sequencing of the PAX6 gene and quantitative analysis of the PAX6 locus allow for efficient molecular genetic evaluation of the clinical diagnosis of both isolated and syndromic aniridia. In cases of clinical overlap with other entities, high-throughput sequencing of multiple additional genes can simultaneously cover genes for differential diagnoses (e.g. microphthalmia syndromes). Optimal care of aniridia patients requires close cooperation of ophthalmologists and medical geneticists.