Abstract: Pharmacometabolomics,stemming from metabolomics,is one of the most recently emerged “-omics” sciences.It can be applied to monitor drug-related alternation in metabolic pathways and predict the therapeutic outcome by comparing the pre- and post-treatment metabolite profiles under the assistance of modern instrumental analysis,chemometricsand bioinformatics.This review summarized the recent progress in pharmacometabolomics and its applications.The critical technical points and pitfalls involved in pharmacometabolomic pipeline were also discussed.