Cloacae and peritoneal canals of species of Testudines, Crocodylia, and Aves were analyzed with the purpose of identifying and describing their morphology and investigating their possible relationship with other cloacal structures. Studies were conducted from dissections and routine histological preparations. The cloaca is located in the pelvic cavity and differs between Testudines and Crocodylia. In the former, the cloaca is divided into three compartments—the coprodeum, urodeum, and proctodeum—without folds separating them. In contrast, in Crocodylia the coprodeum, urodeum, and proctodeum are separated by discrete folds, the coprourodeal and uroproctodeal folds. The visceral layer of the peritoneum forms the peritoneal canal and also differs in Testudines and Crocodylia. In the former, the cranial opening of the peritoneal canal is lateral to the urogenital sinus and the canal is caudally projected into the phallus, laterally followed by the ejaculatory groove until the caudal end of the organ. In Crocodylia, the cranial opening of the peritoneal canal is lateral to the coprodeum and the canal extends caudally until reaching a papilla in the body of the phallus, where it terminates. Histologically, the mesothelium of the peritoneal canal has a simple pavement appearance. In Testudines, regions with a simple cubic epithelium were found, indicating intense cell activity. The lamina propria is characterized by a thickening of the connective tissue, moderately dense with a variable thickness and with a layer of bundles of smooth muscle arranged in different directions. In Caiman yacare, bundles of striated skeletal muscles were found on the loose connective tissue that involves the peritoneal canal. The cloacal and peritoneal fluids have a strong protein similarity. The peritoneal canal reflects functional characteristics related to reproduction. No peritoneal canals were found in birds.