Mutations in the CHD7 (chromodomain helicase DNA binding protein 7) gene cause CHARGE syndrome. At present, however, genetic testing of the CHD7 gene is not commonly applied in clinical settings because the currently available assays are technically and financially demanding, mainly because of the size of the gene. In the present study, we optimized the highly sensitive and specific mutation scanning method automated denaturing high-performance liquid chromatography (DHPLC) to analyze the entire coding region of CHD7. The coding region was amplified by 39 primer pairs, all of which have the same cycling conditions, aliquoted on a 96-well format polymerase chain reaction (PCR) plate. In this manner, all of the exons were amplified simultaneously using a single block in a thermal cycler. We then wrote a computer script to analyze each segment of the CHD7 gene by DHPLC in a serial manner using conditions that were optimized for each amplicon. The implementation of this screening method for CHD7 will help medical geneticists confirm their clinical impressions and provide accurate genetic counseling to the patients with CHARGE syndrome and their families.