A high-capacity low-cost mutation scanning method based on denaturing high-performance liquid chromatography (DHPLC) has been recently introduced. We have implemented an automated and cost-effective strategy using DHPLC. To facilitate the semi-automated analysis of multiple exons, two steps were taken. The first step was the development of a PCR protocol for the amplification of multiple exons under the same conditions. Primer sets, which amplify each exon in the entire gene, were aliquoted to and air-dried on a 96-well format PCR plate. In this way, all the exons in a gene can be simultaneously amplified on a single PCR machine. The second step was the serial DHPLC analysis of multiple amplicons under conditions optimal for each amplicon. We named the 96-well plate containing the primer pairs and the corresponding computer file used to analyze each amplicon under the pre-determined optimal conditions as the "Condition-Oriented-PCR primer-Embedded-Reactor plate," or the COPPER plate. We have developed COPPER plate systems for more than 20 congenital disorders including classic congenital syndromes like Marfan syndrome (FBN1: 65 amplicons), CHARGE syndrome (CHD7: 39 amplicons), de Lange syndrome (NIPBL: 46 amplicons), Sotos syndrome (NSD1: 30 amplicons), and Rubinstein-Taybi syndrome (CREBBP: 41 amplicons). Using the COPPER plate system, we are functioning as a reference laboratory for the clinical molecular diagnosis of congenital malformation syndromes and are presently analyzing more than 200 samples annually from all over Japan.