A 10-month-old female toy poodle was referred to the University of Tokyo Veterinary Medical Center with a urogenital anomaly found during sterilization. An exploratory laparotomy revealed a cyst adhering to the cervix and a unilateral renal agenesis. Histopathology and immunohistochemical analysis of the cyst was consistent with remnants of the Wolffian duct or a Gartner duct cyst. This is a rare case of a canine Gartner duct cyst with renal agenesis and uterine anomaly. We discuss the similarity of this case to that of humans and introduce a classification in the literature for these complex urogenital malformations for further clinical research into the precise diagnosis and appropriate surgical planning.