At one point in the development of the human embryo, there is a cloaca. It is the far end of a structure called the hindgut. This structure then divides to form a rectum, a bladder, and genitalia. Persistent cloaca is a defect in which the rectum, vagina and urinary tract are connected into a single common channel. Cloacal malformations result when a baby girl's vagina, urinary tract, and anus do not separate from one another completely.