Cancers arising within the gastrointestinal (GI) tract are commonly associated with an immune component at their inception and later in their maintenance. While many of the immune factors and immune cell types surrounding these lesions have been highlighted, the underlying pre-dispositions in immunesupported carcinogenesis are not well characterised. Inherited Mendelian GI disorders such as polyposis syndromes, while classically due to germline mutations in non-immune genes, commonly demonstrate alterations in key immune and inflammatory genes. In some cases immune based therapies have been shown to provide at least some benefit in animal models of these syndromes. The advent of genome wide association studies has begun to powerfully examine the genetic nature of complex non-Mendelian GI diseases highlighting polymorphisms within immune related genes and their potential to provide the niche in which GI cancers may originate. Here in the role in which Mendelian and non-Mendelian genetics of immune related factors supporting GI malignancy will be presented and discussed.