Genetic differences among individuals can explain some of the variability observed during drug treatment. Many studies have correlated the different pharmacological response to genetic variability, but most of them have been conducted on adult populations. Much less attention has been given to the pediatric population. Pediatric patients constitute a vulnerable group with regard to rational drug prescribing since they present differences arising from the various stages of development. However, only a few steps have been made in developmental pharmacogenomics. This review attempts to describe the current methods for pharmacogenetic and pharmacogenomic studies, providing some of the most studied examples in pediatric patients. It also gives an overview on the implication and importance of microRNA polymorphisms, transcriptomics, metabonomics, and proteomics in pharmacogenetics and pharmacogenomics studies.