Endometriosis is defined as the growth of endometrial glands and stroma in ectopic locations. Its aetiology is multifactorial, but autoimmunity has been shown to play a role in its onset and development. The present study aimed to investigate the presence of both IgG and IgM anti-endometrial antibodies in sera of endometriosis patients in comparison with age-matched controls, and to also investigate the cognate endometrial proteins involved. Sera from these groups were screened by western blot and immunohistochemistry. Thirteen out of the 40 sera tested were positive for IgG isotype, and 10/27 IgG negative patients were positive for IgM isotype. These findings indicate that endometrial antibodies of IgG and IgM classes could be detected in almost 60% of endometriosis patients. Of the various identified endometrial antigens, 30 and 45 kDa antigens were immunodominant in both IgG and IgM positive endometriosis patients. With immunohistochemistry, positive sera showed reactivity in luminal epithelium, glandular epithelium and stroma. These anti-endometrial antibodies might be partially responsible for failure of implantation leading to infertility. Identification of specific targets would be a help in understanding the pathophysiology of endometriosis, and would also help in setting up a non-invasive test for the diagnosis of endometriosis.