We developed a simple and rapid single nucleotide polymorphism (SNP) detection system named SMart Amplification Process (SMAP). SMAP is an isothermal nucleic acid amplification method, which uses novel Aac DNA Polymerase isolated from Alicyclobacillus acidocaldarius. Aac DNA Polymerase is in particular suitable isothermal amplification processes having a strand displacement activity. Moreover, SMAP employs an asymmetrical primer design and uses Thermus aquaticus MutS (Taq MutS). Taq MutS is a mismatch binding protein providing a highly effective approach to achieving complete suppression of background amplification derived from mis-amplified DNA. Therefore DNA amplification only occurs with a perfect primer match, and amplification alone is sufficient to identify the target allele. These features of SMAP enable us to perform rapid and precise SNP detection assays. SMAP has immense potential for the development of medical diagnostic products, as for example, to rapidly detect EGFR or K-ras gene mutations at high accuracy. The development of molecular diagnostics along with an increasing knowledge about genomic information has caused a paradigm shift away from the standard protocol of medical care towards pharmacogenomics. This new field of medical science is based on the growing knowledge about genetic alterations and their relationship to specific phenotypes, such as disease predisposition, drug metabolism, and disease development. Due to its ability for high-throughput gene analysis and SNP detection, SMAP is certain to have significant impact in this field.