The information gained from pharmacogenomic testing is becoming increasingly recognized as an opportunity to improve our current dosing strategies for children. The identification of gene polymorphisms that influence drug disposition and effect can be used to help predict a child's susceptibility to toxicity and/or response to a particular drug or therapeutic regimen. However, the potential consequences of performing genomic analysis in children raise important ethical considerations. Although the level of risk introduced remains partially hypothetical, awareness of the ethical concerns and protective legislation will be an important part of fully informing patients, families, clinicians, and researchers about the risks and benefits of pharmacogenomic testing in children. Where it can be done without loss of benefit, risk reduction is a moral imperative, and so the ethical complexities related to pharmacogenomics must be addressed in an ongoing way as we continue to learn more about the value of the technology to children.