The purpose of this review is to describe the state of the art of the pharmacological applications in perinatal medicine and highlight how a new emerging discipline, metabolomics, may have a significant impact on understanding complex biological processes associated with the drugs actions. Currently, there is great demand for new information regarding the use of drugs, especially during the perinatal period in order to minimize the occurrence of adverse drug reactions and to maximize the desired therapeutic effect. Metabolomics is a functional genomic tool concerned with the high-throughput identification, quantification and characterization of small molecule metabolites. This new technique has been shown to have a great impact on classifying phenotypes, investigation of physiological status, diagnosing disease, measuring the response to treatment, discovering biomarkers, and identifying perturbed pathways due to disease or treatment. Metabolic profiles appear to be a key factor in predicting the outcome of a pathological condition and the individual’s response to a pharmacological treatment. This new systems biology tool may have important potential implication for pharmacological science, in particular drug discovery, development, and prediction of the drug’s effects on the body by explaining the mechanisms by which drug response causes adverse effects.