The vagina is just cranial to the anus and both are found in a common urogenital slit. In most cetaceans the urogenital opening is quite caudal in comparison to the penile opening in males (see sex determination section for more information).   The vagina is thick-walled and terminates at the thick, muscular cervix. The uterus in marine mammals is bicornuate (or bipartite in phocids), meaning it has two horns. Like in other mammals, the egg matures in the ovary, is released into the fallopian tube, and then travels down the tube. If sperm are present, conception may occur and the fetus will develop in one horn of the uterus.

Some of the most useful life history data can be gathered by examination of the reproductive tract. Examination of the ovary for the presence of corpus luteum (yellow-brown scar) or corpus albicans (white scar) can indicate ovulatory events.  The corpus luteum can indicate recent ovulation while the corpus albicans indicates past ovulatory events. Presence of either of these indicates a mature female. At necropsy, both ovaries should be fixed whole and later examined to count the number of corpora present before being cross sectioned. The uterus may be opened up and examined or may be fixed whole in a large container to preserve the natural shape of the structure. Additional evidence of past pregnancies may be found by examining the uterine walls and looking for scaring. The placenta will leave a scar on the uterine wall for several months after the female has given birth.

Additional information on necropsy sampling techniques and the female reproductive tract in cetaceans can be found in the The CRC Handbook of Marine Mammal Medicine (Dierauf and Gulland Eds., 2001) or in The Biology of Marine Mammals (Reynolds and Rommel Eds., 1999).