Here we report that an EMT regulator SIP1 is a target of the Hh signal in gastric pit cells and in diffuse-type GC, and that SIP1 regulates mesenchymal-related genes (WNT5A, CDH2, PDGFRB, EDNRA, ROBO1, ROR2, and MEF2C), which express preferentially in both pit cell and diffuse-type GC. This evidence concerns the gene WNT5A and gastric cancer.