Purpose, This study was performed to investigate the expression pattern of Wnt inhibitory factor 1 (Will) and beta-catenin during anorectal development in normal and anorectal malformation (ARM) embryos and the possible role of Wifl and beta-catenin in the pathogenesis of ARM, Methods. ARM was induced with ethylenethiourea on the 10th gestational day in rat embryos. Cesarean deliveries were performed to harvest the embryos, The expression pattern of Wifl and beta-catenin protein and mRNA was evaluated in normal rat embryos (n = 288) and ARM rat embryos (n= 306) from GD13 to GD16 using immunohistochemical staining, Western blot, land real time RT-PCR, Results, Immunohistochemical staining revealed that in normal embryos Wifl was constantly expressed in the cloaca from GD13 to GD16, On GD13 and GD14, Wifl immunopositive cells were extensively expressed in the cloaca. On GD15, the expression of Wifl were mainly detected on the very thin anal membrane. In ARM embryos, the epithelium of the hindgut and urorectal septum demonstrated faint immunostaining for Wifl from GD14 to GD16. Western blot and real time RT-PCR revealed that Wifl and beta-catenin protein and mRNA expression level was significantly decreased in the ARM groups compared with the normal group on GD14 and GD15 (p < 0.05). Conclusions. This study demonstrated that the expression pattern of Wifl and beta-catenin was disrupted in ARM embryos during anorectal morphogenesis, which demonstrated that downregulation of Wifl and beta-catenin at the time of cloacal separation into the primitive rectum and urogenital septum might related to the development of ARM.