Endometriosis is a chronic inflammatory condition affecting 5–10% of reproductive-aged women, characterized by the growth of endometrial-like tissue outside the uterus, leading to pelvic pain and infertility. Despite its prevalence, the underlying molecular mechanisms are poorly understood. Current treatments focus on suppressing lesion activity rather than eliminating them. Endometriosis is associated with an increased risk of specific subtypes of ovarian cancer, suggesting shared molecular pathways with cancer. Advances in single-cell and spatial genomics, along with organoid models, have begun to elucidate the molecular mechanisms of endometriosis. This review summarizes key genetic mutations and alterations driving the development and progression of endometriosis to malignancy, recent advances in understanding the molecular basis, and novel approaches and in vitro models for improving diagnosis and treatment. Endometriosis affects 5–10% of reproductive-aged women, causing pelvic pain and infertility. It is characterized by the presence of endometrial tissue outside the uterus, most commonly on the ovaries, fallopian tubes, and pelvic peritoneum. Endometriosis is difficult to diagnose due to varying symptoms, and there is no universally validated diagnostic test. Treatment options are limited, focusing on controlling symptoms rather than curing the disease. Endometriosis is classified into three subtypes: superficial peritoneal endometriosis (SUP), deep infiltrating endometriosis (DIE), and ovarian endometriosis (endometriomas). The origin of endometriosis is still debated, with retrograde menstruation and stem cell origin theories being the most studied. Genetic and environmental factors contribute to the development of endometriosis, and recent studies have identified several risk loci and candidate genes involved in steroid hormone imbalance and neoplastic characteristics. Endometriosis is associated with an increased risk of ovarian cancer, and specific subtypes of ovarian cancer, such as endometrioid carcinomas, are strongly linked to endometriosis. Advances in 3D organoid models, single-cell omics, and imaging techniques are providing new insights into the disease pathology and potential therapeutic targets.Endometriosis is a chronic inflammatory condition affecting 5–10% of reproductive-aged women, characterized by the growth of endometrial-like tissue outside the uterus, leading to pelvic pain and infertility. Despite its prevalence, the underlying molecular mechanisms are poorly understood. Current treatments focus on suppressing lesion activity rather than eliminating them. Endometriosis is associated with an increased risk of specific subtypes of ovarian cancer, suggesting shared molecular pathways with cancer. Advances in single-cell and spatial genomics, along with organoid models, have begun to elucidate the molecular mechanisms of endometriosis. This review summarizes key genetic mutations and alterations driving the development and progression of endometriosis to malignancy, recent advances in understanding the molecular basis, and novel approaches and in vitro models for improving diagnosis and treatment. Endometriosis affects 5–10% of reproductive-aged women, causing pelvic pain and infertility. It is characterized by the presence of endometrial tissue outside the uterus, most commonly on the ovaries, fallopian tubes, and pelvic peritoneum. Endometriosis is difficult to diagnose due to varying symptoms, and there is no universally validated diagnostic test. Treatment options are limited, focusing on controlling symptoms rather than curing the disease. Endometriosis is classified into three subtypes: superficial peritoneal endometriosis (SUP), deep infiltrating endometriosis (DIE), and ovarian endometriosis (endometriomas). The origin of endometriosis is still debated, with retrograde menstruation and stem cell origin theories being the most studied. Genetic and environmental factors contribute to the development of endometriosis, and recent studies have identified several risk loci and candidate genes involved in steroid hormone imbalance and neoplastic characteristics. Endometriosis is associated with an increased risk of ovarian cancer, and specific subtypes of ovarian cancer, such as endometrioid carcinomas, are strongly linked to endometriosis. Advances in 3D organoid models, single-cell omics, and imaging techniques are providing new insights into the disease pathology and potential therapeutic targets.