Recent advances in the comprehension of pathogenic mechanisms of human diseases have brought the researchers to the discovery of putative pharmacological targets and the subsequent development of the so-called targeted drugs. In order to maximize their efficacy, as well as that of the other drugs, it is imperative to identify those patients that are more prone to experience a therapeutic benefit. In the pharmacogenetic area, several strategies may be pursued to assay biomarkers. The quantitation of gene expression, the identification of changes in gene and chromosomal sequences, and the evaluation of epigenetic factors may contribute to anticipate drug efficacy and tolerability. At those levels, the number of candidate genes that may be investigated is highly variable, up to the evaluation of the whole human genome. Despite the increasing complexity of pharmacogenetic analyses and their interpretation, some relationships between genetic biomarkers and treatment outcomes may be characterized by suboptimal values of sensitivity and specificity. For that reason, the validation of the biomarkers and their transfer into the clinics are the major challenges.