Single nucleotide polymorphisms (SNPs) have been suggested as a useful tool for dissecting various human complex disorders, classically at a small scale and recently at large genome-wide levels. The advent of new technologies, including chip-based genotyping as well as high-throughput next generation sequencing, has opened new avenues for SNPs to be used in clinical practice. In this chapter, we summarize the current use of SNPs mainly SNP-based arrays in various clinical applications as well as describe the classical and recent methods of SNP detection and genotyping currently being used in the research and clinical environments.