Throughout recent decades, the incidence of preterm birth has risen worldwide, and although the majority of preterm neonates now survive infancy, many suffer from debilitating morbidities in the short term and/or increased disease risks in the long term. Traditional diagnostic biomarkers suffer from considerable confounders, limiting their use in the early identification of diseases. There is a need to develop novel biomarkers that can identify, in real time, the evolution of organ dysfunction in an early diagnostic, monitoring, and prognostic fashion. Use of "omics," particularly metabolomics, may provide valuable information regarding functional pathways underlying different pathologies and prediction of clinical outcomes. The emerging knowledge generated by the application of metabolomics in neonatology provides new insights that can help to identify markers of early diagnosis, disease progression, response to treatment, and new therapeutic targets. In this chapter, we review the current knowledge of different metabolomics technologies in neonatal-perinatal medicine, including biomarker discovery, defining as yet unrecognized biologic therapeutic targets, and linking of metabolomics to relevant standard indices and long-term outcomes.