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Understanding the immune system’s role in endometriosis onset is critical for disease prevention. Our mathematical model explores how innate immune cells interact with endometrial cells during early stages of disease onset. Our findings indicate endometrial cell presence in the pelvic cavity alone is insufficient to cause endometriosis. Rather, a reduction in immune cell cytotoxicity is a more likely cause of disease. We predict that a decline in immune function (cytotoxicity or endometrial cell detection) can result in endometriosis onset, and a significant improvement in function is then required for disease recovery. This work provides valuable insight into understanding endometriosis onset.