Background: The oncological outcome of surgery for the treatment of pelvic malignancies can be improved by performing pelvic lymphonodectomy. However, the extent and regions of lymph node harvest are debated and require profound knowledge of anatomy in order to avoid collateral damage. Methods: The embryological development and topographic anatomy of pelvic compartments in relation to pelvic lymphonodectomy for rectal, uterine, and prostate cancer are reviewed. Based on pre-dissected anatomical specimens, lymph node regions and drainage routes of the posterior and urogenital pelvic compartments are described in both genders. Anatomical landmarks are highlighted to identify structures at risk of injury during pelvic lymphonodectomy. Results: The ontogenesis of urogenital and anorectal compartments and their lymphatic supply are key factors for adequate lymphonodectomy, and have led to compartment-based surgical resection strategies. However, pelvic lymphonodectomy bears the risk of injury to somatic and autonomic nerves, vessels, and organs, depending on the regions and extent of surgery. Conclusion: Embryologically defined, compartment-based resection of pelvic malignancies and their lymphatic drainage routes are based on clearly delineated anatomical landmarks, which permit template-oriented pelvic lymphonodectomy. Comprehensive knowledge of pelvic anatomy, the exchange of surgical concepts between specialties, and minimally invasive techniques will optimize pelvic lymphonodectomy and reduce complications.