Endometriosis is a benign, common, but controversial disease due to its enigmatic etiopathogenesis and biological behavior. Recent studies suggest multiple genetic, and environmental factors may affect its onset and development. Genomic analysis revealed the presence of cancer-associated gene mutations, which may reflect the neoplastic aspect of endometriosis. The management has changed dramatically with the development of fertility-preserving, minimally invasive therapies. Diagnostic strategies based on these recent basic and clinical findings are reviewed. With a focus on the presentation of clinical cases, we discuss the imaging manifestations of endometriomas, deep endometriosis, less common site and rare site endometriosis, various complications, endometriosis-associated tumor-like lesions, and malignant transformation, with pathophysiologic conditions.