Metabolomics consists of the quantitative analysis of a large number of low molecular mass metabolites involving substrates or products in metabolic pathways existing in all living systems. The analysis of the metabolic profile detectable in an human biological fluid allows to instantly identify changes in the composition of endogenous and exogenous metabolites caused by the interaction between specific physiopathological states, gene expression, and enviroment. In pediatrics and neonatology, metabolomics offers new encouraging perspectives for the improvement of critically ill patients outcome, for the early recognition of metabolic profiles associated with the development of diseases in the adult life, and for delivery of individualized medicine. In this view, nutrimetabolomics, based on the recognition of specific cluster of metabolites associated with nutrition and pharmacometabolomics, based on the capacity to personalize drug therapy by analyzing metabolic modifications due to therapeutic treatment may open new frontiers in the prevention and in the treatment of pediatric and neonatal diseases. This review summarize the most relevant results published in the literature on the application of metabolomics in pediatric and neonatal clinical settings. However, there is the urgent need to standardize physiological and preanalytical variables, analytical methods, data processing, and result presentation, before to establish the definitive clinical value of results.