Objective(s): Adenomyosis and endometriosis are two different diseases, although they have similar pathogenesis and characteristic. The serum differential expressed proteins in adenomyosis and endometriosis may result from the different pathogenesis of two diseases. Proteomic technology is a useful method for detecting all the proteins in samples. We try to use isobaric tags for relative and absolute quantitation (iTRAQ) technology to explore the association between the potential pathogenesis of these two diseases and these identified proteins. Study design: The serum samples from 20 patients with adenomyosis and from 20 patients with endometriosis were analyzed using iTRAQ technology to detect the differential expression of proteins. The validation of the proteins was performed using Western blot. Results: In the serum of women with adenomyosis and with endometriosis, 14 proteins were found differentially expressed using iTRAQ technology. Nine proteins were high-expression in adenomyosis group and four proteins increased in endometriosis group. And the differential expression proteins were validated by Western blot. Conclusion(s): The proteins increased in adenomyosis group are related to blood coagulation and complement activation effects, and the proteins high-expression in endometriosis mainly take part in the process of inflammatory response and regulation of apoptosis. The differentially expressed proteins in two groups may due to the different pathogenesis of two diseases. (C) 2014 Elsevier Ireland Ltd. All rights reserved.