Systems biology attempts to elucidate the complex interaction between genes, proteins and metabolites to provide a mechanistic understanding of cellular function and how this function is affected by disease processes, drug toxicity or drug efficacy effects. Global metabolic profiling is an important component of systems biology that can be applied in both preclinical and clinical settings for drug discovery and development, and to study disease mechanisms. The metabolic profile encodes the phenotype, which is composed of the genotype and environmental factors. The phenotypic profile can be used to make decisions about the best course of treatment for an individual patient. Understanding the combined effects of genetics and environment through a systems biology framework will enable the advancement of personalized medicine.