The polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis is considered as one of useful routine genetic analyses. However, that PCR-SSCP has been analyzed using radioisotope (RI) such as [32P] labeled compounds. So that, it was difficult to use this method routinely at clinical laboratories. In this paper, we compared with an RI mediated and a non-RI coloration mediated PCR-SSCP analysis regarding to those of sensitivity, time and money cost, respectively. The coloration method had enough sensitivity to detect one of cholesteryl ester transfer protein gene mutations. The time and money cost of non-RI coloration mediated method were more advantageous than the RI mediated one. Therefore, it is shown that the non-RI coloration mediated PCR-SSCP analysis is very useful for the routine genetic analysis at clinical laboratories.