Today, disorders that affect the newborn remain a challenge for physicians because of the enigmatic pathophysiology and difficulties in treating such delicate patients. Metabolomics, the “omics” science that studies the metabolome, namely the metabolites present in biological fluids, such as saliva, blood, sweat, and breast milk in a given time or condition, can be useful in helping neonatologists to prevent, diagnose, and treat diseases affecting the neonate, especially those with higher mortality rates. Since it is a relatively new technology, studies of its application in neonatology are limited. The aims of this review are to present metabolomics data on relevant neonatal disorders and to identify and discuss the most important 5 metabolites and their clinical significance rather than focusing on each disorder. The preliminary data are promising but further studies on metabolomics in neonatology are needed together with the standardization of results before their application in clinical practice.