We studied endometrial structure and ultrastructure in serial biopsy specimens from patients with endometriosis treated with danazol (N = 19) or intranasal buserelin (N = 13) for 6 months. Biopsies were performed before and at 3 and 6 months of treatment. The specimens were studied by light, scanning, and transmission electron microscopy. Six morphometric indices were evaluated. Danazol produced a progestational effect on endometrial glands and stroma associated with marked hypotrophy of the mucosa, and buserelin treatment resulted in weakly proliferative or inactive mucosa. Both drugs induced noncyclicity and hypotrophy of endometrium although with different mechanisms of action, and it is suggested that they may have similar effects on ectopic endometrium. Because the atrophic effect of danazol appeared earlier than that of buserelin, the former could be recommended for short-term therapy.