The mammalian intestinal epithelium is one of the most actively self-renewing tissues, which is constantly replenished by pluripotent intestinal stem cells (ISCs). This remarkable characteristic seems to impact in its high propensity for malignant transformation. Indeed, many of the molecular pathways that regulate normal intestinal homeostasis appear involved in colorectal carcinogenesis. Inactivating mutations of the APC (Adenomatous Polyposis Coli) gene is a hallmark of colorectal cancer. The main tumor suppressive function of Apc is to negatively regulate Wnt signaling. Targeted deletion of Apc in the murine intestine, and more recently in the zebrafish gut, recapitulate many aspects of the human disease. Work in Drosophila now reveals that the role of APC in the intestine is ancient and highly conserved across species. In support of these findings, we present data which suggests that APC1 may be a marker for adult ISCs in Drosophila and is required specifically within the ISCs to regulate intestinal homeostasis. Here we discuss the similarities and differences between these model organisms in regards to the role of Wnt signaling and APC in intestinal homeostasis and transformation.