Pharmacogenomics is the study of the genetic basis of individual variation in response to therapeutic agents. Pharmacogenomics may potentially affect on every step of health care and every drug treatment protocol. The optimal approach to pharmacogenomics in hypertension requires the integration of different disciplines, in which biomedical informatics plays an essential role. This chapter describes biomedical informatics methods used in dealing with key issues in pharmacogenomics. These key issues include the association between structure and function, the interaction between gene and drug, and the correlation between genotype and phenotype. Heterogeneous resources, including web sites, databases, and software analysis tools, are selected, organized, and integrated in practical methods to support these studies. Bioinformatics methods described in this chapter include genetic sequence searching, comparison, structural modeling, functional analysis, and systems biology studies, with emphasis on single-nucleotide polymorphism (SNP) analysis. Medical informatics methods such as disease and drug information and clinical terminology are also embraced in this chapter. This combination of both biological and medical informatics provides comprehensive methodologies to resolve complex problems in pharmacogenomics.