Background: Endometriosis is one of the most common causes of infertility and pelvic pain. A baboon model has recently been developed whereby the intrapelvic injection of menstrual endometrium results in the induction of endometriotic lesions. We have used this model to investigate changes in ultrastructure and glycosylation of endometria from normal and diseased baboons. Methods: Endometriosis was induced ineight female baboons; endometrial tissue and endometriotic lesions were removed on days 9-11 post ovulation between 3 and 16 months of disease and compared with endometrium from 17 control animals, using electron microscopy and lectin histochemistry. Result: Ultrastructurally, diseased endometrial glands showed abnormalities in secretory vacuoles and an intracellular accumulation of glycogen; in later stages of the disease, glands resembled those of the late secretory phase endometrium. The abnormalities were mirrored by changes in glycan expression. In early disease, there was an increased binding of lectin from Dolichos biflorus agglutinin (DBA) to fucosylated N-acetylglucosamine residues, whereas in later stages, this binding generally decreased in association with the appearance of a late secretory phenotype. Conclusions: Endometriosis is accompanied by progressive changes in the gland architecture and biochemistry resulting in dyssynchrony within the window of uterine receptivity, which may result in the reduced fertility associated with this disease. © 2006 Oxford University Press.