The youngest and more rapidly increasing "omic" discipline, called metabolomics, is the process of describing the phenotype of a cell, tissue or organism through the full complement of metabolites present. Metabolomics measure global sets of low molecular weight metabolites (including amino acids, organic acids, sugars, fatty acids, lipids, steroids, small peptides, vitamins, etc.), thus providing a "snapshot" of the metabolic status of a cell, tissue or organism in relation to genetic variations or external stimuli. The use of metabolomics appears to be a promising tool in neonatology. The management of sick newborns might improve if more information on perinatal/neonatal maturational processes and their metabolic background were available. Urine ("a window on the organism") is a biofluid particularly suitable for metabolomic analysis in neonatology because it may be collected by using simple, noninvasive techniques and because it may provide valuable diagnostic information. In this review, the authors report the few literature data on neonatal metabolomics, including their personal experience, in the following fields: intrauterine growth restriction, perinatal transition, asphyxia, brain injury and hypothermia, maternal milk evaluation, postnatal maturation, bronchiolitis, sepsis, patent ductus arteriosus, respiratory distress syndrome, nephrouropathies, metabolic diseases, antibiotic treatment, perinatal programming and long-term outcome in extremely low birth-weight infants.