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Genome-wide association studies (GWAS) have been successfully performed to identify variants associated with complex diseases.Meanwhile, the application of GWAS to Pharmacogenomics researches which focus on the analysis of associations between genotype and phenotype in pharmacogenomics-related traits have found amount of loci that affect either drug response or susceptibility to adverse drug reactions.Although the effect size and sample size in the Genome-wide pharmacogenomic Studies are smaller than the GWAS of complex diseases, the results demonstrate the importance of multiple genetic factors combined with clinical features.It can investigate new insights into mechanisms of drug action or toxicity, and as a result can contribute to the development of new therapeutic agents.This report discusses the advantage, the challenges and the future direction in GWAS analysis of pharmacologic studies.