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In the early 21st century, the stem cell theory of endometriosis pathogenesis has offered new insights into its diagnosis and treatment. The stem cell theory posits that the terminal cells in the ectopic lesions are unable to sustain the long\u2010term development of the lesions. Instead, endometrial stem cells (SCs) and SCs from outside the uterus are believed to participate in the formation and development of endometriosis. Notably, mesenchymal SCs (MSCs), which are multipotent SCs derived from the mesoderm, may contribute to the progression and potential malignant transformation of endometriosis through specific mechanisms. Therefore, this paper outlines the pathogenesis of endometriosis and the discovery of the stem cell theory. 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