Endometriosis is a chronic recurrent disease that is relatively common. Diagnosis is difficult and often delayed. Current treatments are inadequate with unacceptable side effects and multiple surgeries may be needed. Abnormal eutopic endometrium may play important role in endometriosis-associated infertility. This study aimed to examine the ultrastructural changes in eutopic endometrium in a rat model of surgically induced endometriosis. Endometrial tissue was removed from rats in surgical endometriosis induction group (n=10), sham operated (n=10) and non-operated control (n=10) groups in the diestrus phase of the estrus cycle. They were studied with light, transmission and scanning electron microscope as well as morphometric analysis. Eutopic endometrium in surgically induced endometriosis showed pseudostratified epithelium, vacuolated columnar cells alternated with dark cells. The stroma was edematous exhibiting dilated, congested blood vessels. The mean endometrial mucosal depth and surface epithelial height significantly increased. Ultrastructurally, most luminal epithelial cells showed vacuolation. Mucous secretory granules were surrounded by dilated rough endoplasmic reticulum cisternae. Mitochondria, glycogen deposits and vesicles with electron dense cores were observed. The nuclei were highly euchromatic. Well defined microvilli were noticed with evident apical tight junctions. Scanning electron microscope revealed flattened and structurless surface epithelium with apparent decrease in the number of pinopodes. A different response to sex hormones in different parts of eutopic endometrium was observed. Ultrastructural features of estrogen dominance or progesterone resistance in the eutopic endometrium might account for inappropriate cyclic changes occurring in the disease.