Maximizing drug response while minimizing adverse effects for individuals through the study of gene variations is the goal of pharmacogenomics. The most common type of human genetic variation is the Single nucleotide polymorphism (SNP), a position at which two alternative bases occur at appreciable frequency (>1%) in the human population. There are three major phases to SNP pharmacogenomics: SNP discovery and mapping, SNP scoring, and SNP diagnostics. Among these, the scoring step holds the greatest potential for uncovering medically important information. This step necessitates applying high-throughput SNP genotyping methods in the context of well-designed clinical pharmacogenetics correlation studies. This chapter presents the basic principle of the methods employed for SNP allele discrimination and detection. Most methods currently adopted require a preliminary amplification, by the polymerase chain reaction (PCR), of a small DNA fragment around the SNP to be analyzed.