Aim: To develop a diagnostic DNA chip to detect mutations in the bigh3 gene causing the most common corneal dystrophies (CDs). Methods: Samples from 98 people, including patients with bigh3-associated CDs (b-aCDs), were examined. Specific primer and probe sets were designed to examine exons 4 and 12 of the bigh3 gene, in order to identify mutant and wildtype alleles. Mutations were then identified by hybridisation signals of sequence-specific probes immobilised on the slide glass. Results: Direct sequencing of exons 4 and 12 of the bigh3 gene in the patients’ genome showed that b-aCDs could be mainly classified into five types: homozygotic Avellino corneal dystrophy (ACD), heterozygotic ACD, heterozygotic lattice CD I, heterozygotic Reis–Bucklers CD and heterozygotic granular CD. Blind tests were performed by applying the target DNA amplified from the genomic DNA isolated from the peripheral blood of the participants onto a DNA chip. The results obtained by DNA chip hybridisation matched well with the direct DNA sequencing results. Conclusions: The DNA chip developed in this study allowed successful detection of b-aCDs with a sensitivity of 100%. Mutational analysis of exons 4 and 12 of the bigh3 gene, which are the mutational hot spots causing b-aCDs, can be successfully performed with the DNA chip. Thus, this DNA chip-based method should allow a convenient, yet highly accurate, diagnosis of b-aCDs, and can be further applied to diagnose other types of CDs. ; This work was supported by Medigenes. Further support by the LG Chem Chair Professorship (SYL) is appreciated.