A high throughput metabolite fingerprinting tool based on wooden-tip electrospray ionization mass spectrometry (WT-ESI-MS) has been established for the serum metabolic profiling study of endometriosis with little sample pre-treatment, no chromatography and instrument cycle times of less than 5 min. Serum samples from endometriosis patients and healthy controls were analyzed by direct WT-ESI-MS with a high resolution ESI-Q-TOF-MS. The resulting data were analyzed by multivariate data analysis. MS/MS experiments were carried out to identify potential biomarkers. Global metabolic profiling and subsequent multivariate analysis clearly distinguished endometriosis patients from healthy controls.A total of ten metabolites, up-regulated or down-regulated, were identified which contribute to the progress of endometriosis. These promising identified biomarkers underpin the metabolic pathway including steroid hormone biosynthesis, glycerophospholipid metabolism, sphingolipid metabolism, pyruvate metabolism, bile acid biosynthesis, and androgen and estrogen metabolisms. Considering that a much higher throughput can be obtained without a chromatographic step, the present WT-ESI-MS method could be developed as a fast prognostic or diagnostic method for endometriosis.