Single nucleotide polymorphisms (SNPs) represent the most common form of sequence variation in human DNA. With the completion of the human genome project, SNP genotyping is being undertaken in a large number of pharmacogenomic studies to identify variants associated with responses to specific drugs. The speed at which the goals of pharmacogenomics will be met depends on the development of a large set of SNP markers and a suite of high throughput genotyping methods. A number of methods for high throughput SNP genotyping have been developed. In most studies, a large number of SNPs must be genotyped in a large number of individuals, so the challenge for most laboratories is to find an affordable method that meets the dual requirements of high accuracy and high throughput. In this review, a number of robust genotyping methods currently in use are described, and estimated instrumentation and reagent costs are compared. Although no single genotyping method will suit all applications, the available technology allows pharmacogenomic studies of nearly any scale to be performed. However, advances are still required in genotyping technology to make whole genome genotyping rapid and cost-effective - a critical component of pharmacogenomic studies.