The Müllerian duct gives rise to female reproductive organs, such as the oviduct and uterus. During gestation, the Wolffian duct, which generates male reproductive organs and the kidney, is formed, and the Müllerian duct then elongates caudally along the preformed Wolffian duct. Anatomical separation of these two ducts in chick embryos demonstrated that the Wolffian duct is required for Müllerian duct formation. Likewise, a few reports supported this notion in mice, including studies on Wnt9b mutant mice and Wolffian duct-specific Lhx1 deletion. However, anatomical ablation of the Wolffian duct has not been established in mice. In this study, we addressed the importance of the interaction between these two reproductive ducts, by generating mice that specifically expressed a diphtheria toxin subunit in the Wolffian duct. While this genetic ablation of the Wolffian duct resulted in kidney hypoplasia/agenesis in both male and female mutant mice, the female mutant mice lacked the uterus, which is derived from the Müllerian duct. At mid-gestation, the Müllerian duct was truncated at the level where the mutant Wolffian duct was prematurely terminated, meaning that Müllerian duct elongation was dependent on the preformed Wolffian duct. However, Wnt9b expression in the Wolffian duct and the resultant canonical Wnt activity, as well as Lhx1 expression, were not affected in the mutant mice. These results suggest that the Wolffian duct regulates Müllerian duct elongation by currently unidentified mechanisms that are independent of canonical Wnt signaling or Lhx1 expression.