Pharmacogenomics data can facilitate our understanding of the sources of variability in drug response, which can potentially lead to improved safety and efficacy of drug therapy for individual patients. A key requirement for the development of individualized medicine or personalized therapy is the ability to rapidly and conveniently test patients for genetic polymorphisms and/or mutations. However, in today's world, genotyping technology remains a bottleneck in clinical applications because of its slow speed and high cost. Therefore, we have recently developed a rapid and cost-effective method for SNP detection, named Smart Amplification Process 2 (SmartAmp2), which enables us to detect genetic polymorphisms or mutations in 30-45 min under isothermal conditions without DNA isolation and PCR amplification. This article presents the SNP detection method and its underlying molecular mechanism as well as clinical research applications.