Inflammatory bowel disease (IBD) and colitis-associated cancer are associated with activation of PAK1 (p-21 activated kinase 1). We previously found that total knockout of PAK1 (PAK1KO) reduced tumorigenesis upon AOM/DSS but enhanced tumorigenesis in another model of IBD with total knockout of IL10 (IL10KO). To better understand the specific role of epithelial PAK1, we crossed Pak1 floxed (PAK1fl) with VillinCre mice for a conditional knockout of PAK1 in intestinal epithelia (PAK1CKO). PAK1fl were included as additional controls. Unexpectedly, inflammation and tumorigenesis were greatly reduced in PAK1fl compared to WT or PAK1KO after AOM/DSS treatment. PAK1CKO had higher tumor incidence and counts compared to PAK1fl, but was still lower in comparison to PAK1KO or WT. When crossed with IL10KO mice, PAK1CKO exacerbated the expected hyperproliferative phenotype, resulting in early mouse morbidity. Despite normal Pak1 mRNA expression in PAK1fl colonic lysates, PAK1 protein expression on immunohistochemistry was higher that WT. Both PAK1fl and PAK1CKO mice were more resistant to shifts in microbiome, and remained clustered together compared to WT or PAK1KO. Altogether, our results suggest that floxing itself may have altered Pak1 expression, which conferred protection from AOM/DSS carcinogenesis.