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Does the inclusion of children in pharmacogenomic research raise new ethical issues? Through an exploration of the relevant laws, policies, guidelines and literature, we have identified five areas of concern and assessed their potential impact. These include (1) the difficulty of assessing risk and the ethics of invasive sampling, (2) the consent and assent process, (3) the circumstances under which and to whom the results of trials should be returned, (4) the effect of pharmacogenomics on identifying and treating orphan groups, and (5) the effect of pharmacogenomics on the pediatric drug approval process and patient recruitment. We conclude that while including pharmacogenomics in research projects involving children does indeed raise ethical concerns, none of these are insurmountable, and in fact, pharmacogenomics provides a promising outlook for the development of research that will benefit children.