This opinion is a reply to the following article: Flordellis CS: The emergence of a new paradigm of pharmacogenomics. Pharmacogenomics 6(5), 515–526 (2005). Systems biology is likely to become a leading paradigm in molecular biology in coming decades. In pharmacogenomics, complexity is rapidly increasing as more genomics and proteomics data become available. Tackling this complexity by employing a systems approach seems to be a promising strategy. The introduction of this new paradigm will reshape both professional education and clinical practice. Professionals in medicine and the life sciences must be prepared to adapt to this new approach. However, systems-based pharmacogenomics is unlikely to be ready for clinical application in near future. In order to benefit patients today, the already available options of pharmacogenomics should be carefully implemented in clinical practice as soon as possible. Teaching the current, continuously updated knowledge of pharmacogenomics should not be postponed until the new paradigm arrives.