The polymerase chain reaction with confronting two-pair primers (PCR-CTPP) is a time-saving and inexpensive genotyping method, which is applicable for most single nucleotide polymorphisms (SNPs). To date, we have established PCR-CTPP conditions for tens of SNPs, including duplex genotyping. This paper introduces triplex PCR-CTPP to simultaneously genotype three functional polymorphisms of carcinogen-detoxifying enzymes, NQO1 C609T, GSTM1 null, and GSTT1 null, all of which are reported to have a significant association with smoking-related cancers. We applied this method for 241 non-cancer patients to demonstrate the performance. Among the subjects, the genotype frequency of NQO1 C609T was 35.7% for CC, 44.4% for CT and 19.9% for TT. The null type frequencies of GSTM1 and GSTT1 were 53.4% and 44.0%, respectively. Their distributions were similar to those reported for Japanese by other studies. This is the first paper reporting the success of triplex PCR-CTPP. The polymorphisms applied are useful examples, which could be adopted not only for research purposes, but also for risk assessment of individuals exposed to carcinogenic substances, such as smokers. This convenient genotyping approach has advantages for application in cancer prevention, especially in the Asian Pacific region.