With the exponential increase in publications on DNA markers explaining and/or predicting response to drug therapy, the potential of pharmacogenetic testing of individual patients to optimize drug treatment is expanding. For the identification of pharmacogenetic markers, several techniques can be used. The specific method usually depends on the requirements of the study, ranging from determining one or two single nucleotide polymorphisms (SNPs) in one to ten patients, one or two SNPs in thousands of patients, several thousands of SNPs in an individual patient, or thousands of SNPs in thousands of patients. In this review we identify and evaluate the information present in the literature on genotyping assays that are currently used for pharmacogenetic analyses, and discuss the advantages and disadvantages of these techniques.