Although the histologic diagnosis of endometriosis is usually straightforward, many diagnostic problems can arise as a result of alterations or absence of its glandular or stromal components. The diagnostic difficulty in such cases can be compounded by tissue that is limited to a small biopsy specimen. The appearance of the glandular component can be altered by hormonal and metaplastic changes, as well as cytologic atypia and hyperplasia. Although the last 2 findings are often referred to collectively as “atypical endometriosis,” they should be separately recognized as their premalignant potential likely differs. In some cases, the endometriotic glands are sparse or even absent (stromal endometriosis). The stromal component can be obscured or effaced by infiltrates of foamy and pigmented histiocytes, fibrosis, elastosis, smooth muscle metaplasia, myxoid change, and decidual change. Occasional findings in endometriosis that may raise concern for a neoplasm include necrotic pseudoxanthomatous nodules, polypoid growth (polypoid endometriosis), bulky disease, and venous, lymphatic, or perineural invasion. Inflammatory and reactive changes within, adjacent to, or at a distance from foci of endometriosis can complicate the histologic findings and include infection within endometriotic cysts, pseudoxanthomatous salpingitis, florid mesothelial hyperplasia, peritoneal inclusion cysts, and Liesegang rings. The histologic diagnosis of endometriosis can also be challenging when it involves an unusual or unexpected site. Five such site-specific problematic areas considered are endometriosis on or near the ovarian surface, superficial cervical endometriosis, vaginal endometriosis, tubal endometriosis, and intestinal endometriosis, including the important distinction of an endometrioid carcinoma arising from colonic endometriosis from a primary colonic adenocarcinoma. Finally, endometriotic foci can occasionally be intimately admixed with another process, such as peritoneal leiomyomatosis or gliomatosis, resulting in a potentially confusing histologic appearance.