In the post-genome era, a simple and inexpensive method for diagnostic analysis is in high demand. Cytochrome P450 (CYP) 2D6 is one of the most widely investigated CYPs in relation to genetic polymorphism. Detection of CYP2D6*5 is difficult since long PCR is used. Especially for samples without DNA extraction, the detection is not sensitive enough for population analysis. Therefore, we developed a CYP2D6*5 genotyping method that involves nested long PCR, directly using human whole saliva as a template without DNA extraction. This method will be very useful for genetic diagnoses and can be an efficient tool for individualization of drug therapy in clinical studies.