Pharmacology is the predominant first-line treatment for most pathologies. However, various factors, such as genetics, gender, diet, and health status, significantly influence the efficacy of drugs in different patients, sometimes with fatal consequences. Personalized diagnosis substantially improves treatment efficacy but requires a more comprehensive process for health assessment. Pharmacometabolomics combines metabolomic, genomic, transcriptomic and proteomic approaches and therefore offers data that other analytical methods cannot provide. In this way, pharmacometabolomics more accurately guides medical professionals in predicting an individual’s response to selected drugs. In this chapter, we discuss the potentials and the advantages of metabolomics approaches for designing innovative and personalized drug treatments.