The pathogenesis of Bronchopulmonary dysplasia (BPD) remains poorly understood. It is a multifactorial disease having a genetic-environmental basis. Although attempts have been made to identify a biomarker, none have been validated for clinical use to date. Metabolomics is a promising field of the "omics technologies" that could allow for better understanding of the pathogenesis and underlying mechanisms of BPD as well as facilitate detection of biomarkers. Identification of these biomarkers would improve diagnosis, identify patients in early disease stages and potentially target intervention. This review focuses on the evidence arising from metabolomics and its interaction with microbiomics and pharmacology with respect to pathogenesis and treatment options for this multifactorial complex disease.