To establish a rapid and automatic gene analysis method, we used capillary electrophoresis (CE) for the analysis of the intron 13 microsatellite repeat polymorphism (MRP) of the coagulation factor VIII gene for the diagnosis of hemophilia A. In the analysis of a 20-bp DNA ladder marker, the reproducibility evaluated using the relative standard deviation (RSD) of the relative migration time for one fragment of each fragment were less than 0.01%, whereas the RSDs of the actual migration time of each fragment were 0.1-0.3%. Thus, the appropriate internal standard should be mixed with the sample when CE resolves polymerase chain reaction (PCR) products. We next analyzed the intron 13 MRP evaluated with (CA)n repeats of the factor VIII gene using a 200-bp DNA fragment as the internal standard. The results showed that the PCR products from the intron 13 MRP could be resolved using CE, even with the repeat numbers of 20 and 21, which differ by only 2 bp. These results suggest that CE is a suitable method for analyzing PCR products for gene diagnosis.