Endometriosis and adenomyosis are two frequent diseases closely linked, characterized by ectopic endometrium. Despite their benign nature, endometriosis and adenomyosis impair women's quality of life by causing pain and infertility and an increase in the incidence of gynecological malignancies has been reported. Since the first description of ectopic endometrium in 1860, different attempts have been made to describe, classify and understand the origin of these diseases. Several theories have been proposed to describe the pathogenic mechanism leading to the development of adenomyosis or endometriosis. However, all the hypotheses show some limitations in explaining all the different aspects and manifestations of these diseases. Despite the remarkable progress made over recent years, the pathogeneses of endometriosis and adenomyosis remain unclear. Moreover, because of the lack of standardized protocols and diagnostic criteria in pathology practice it is difficult to study and to classify these disorders. The goal of this review is to summarize the pathological aspects of adenomyosis and endometriosis, spanning a historical perspective to newly reported data.