In recent years there have been unprecedented advances in our understanding of the involvement of genetic polymorphisms in the response to drug therapies. Polymorphisms have been identified that lead to variable patient responses to several medications including cardiovascular, psychiatric, anti-infective and analgesic therapies. The potential for the development of customized, genotype-based therapies is scientifically and clinically attractive. However, these developments, although bearing scientific promise, raise ethical concerns for the conduct of research with human subjects, particularly with respect to confidentiality, risk-benefit analysis, DNA-banking and pharmacoeconomic issues. This article discusses some of the ethical considerations that are related to the use of pharmacogenomics in clinical research protocols.