Following a study in a baboon model of endometriosis, we here describe the morphology of ectopic peritoneal lesions in the human to examine the effects of an ectopic site on glandular structure and function. Ectopic biopsies from 17 women with endometriosis were fixed and processed for electron microscopy. Certain biopsies were also probed for intermediate filaments using immunohistochemistry. Ultrastructurally, lesions showed many different glandular morphologies with indications of delayed maturation compared to normal endometrium. Mesothelium covered some lesions and there was evidence of mesothelial invasion into the stroma. Ectopic endometriotic lesions from women with endometriosis showed ultrastructural differences from eutopic endometrium, with indications that mesothelial invasion may contribute to gland development in some lesions.