Metabolomics is based on the detailed analysis of metabolites and represents a unique chemical fingerprint of an organism. This approach allows assessing the dynamic behavior of biologic systems with multiple network interactions among individual components. The field of metabolic profiling has rapidly developed over the last decade, with successful applications in various research areas including toxicology, disease diagnosis and classification, pharmacology, and nutrition. This article provides a comprehensive account of existing data in the literature from animal and clinical studies on the use of metabolomics for improved understanding of medical conditions affecting the neonate and the developing human being.