AbstractACI rats are distinguished by a polygenic trait resulting in unilateral agenesis of the urogenital system in 20–30% of animals of both sexes. This report details additional features, both morphological and physiological, which distinguish ACI rats with unilateral agenesis of the reproductive and urinary tracts from the majority of ACI rats that have intact urogenital systems. Young female ACI rats were ovariectomized at 34 days of age and sacrificed 19 days later. A preliminary determination of the urogenital morphology was made at the time of ovariectomy and then confirmed by careful abdominal inspection at necropsy. Data on the time of vaginal opening were obtained at selected intervals prior to sacrifice. At necropsy, the mammary glands were removed and were prepared as stained whole mounts for morphological evaluation; the remaining portions of the reproductive tracts were excised, weighed, fixed, and sectioned for microscopic examination. A majority of animals with unilateral agenesis had mammary glands that had higher degrees of glandular proliferation than the mammary glands of intact rats. Unilateral agenesis animals also possessed significantly thicker and heavier uterine horns, despite having been ovariectomized. Furthermore, rats with unilateral agenesis were found to have an earlier time of vaginal opening than that of their intact counterparts. These features of ovariectomized ACI rats with unilateral agenesis are consistent with an active, extra‐ovarian source of endogenous estrogen. Further investigation of the endocrinological state of animals with unilateral agenesis of the urogenital tract is warranted. Those using this model system for transplacental or endocrinological studies should take into account these distinguishing characteristics of ovariectomized ACI rats with unilateral agenesis when planning experiments and analyzing data from a population of rats with both morphologies. © 1992 Wiley‐Lis