Differential proteins expressing in ectopic and eutopic endometria were investigated by means of proteomic analysis. Five patients in secretary phase were diagnosed as endometriosis by laparoscopy. The five ectopic endometria(two at stage II, two at stage III and one at stage IV) and five eutopic endometria were surgically excised. One-dimensional electrophoresis coupled with liquid chromatography and mass spectrometry was used to screen and identify differential proteins. Three differential bands in one-dimensional electrophoresis were resolved by liquid chromatography and mass spectrometry and 14 up-regulated proteins were identified, including collagen α-1, α-2, α-3(VI), α-1(XIV) chain, actin, annexin A2, EMILIN-1, ferritin light polypeptide variant, fucosyltransferase 10, myosin-9, protein S100-A9, KIAA1783 protein, and two hypothetical proteins. Our data provides a list of potential biomarkers for endometriosis. The identifications may be used to develop new diagnoses for endometriosis.