IBD patients have increased chances of developing colorectal cancer. Additionally this specific form of colon cancer is very difficult to treat. Despite numerous efforts we still do not fully understand the relationship between intestinal inflammation and the increased chance for colon cancer development. Understanding this will allow us to develop more specific and targeted prevention measures. Recently, a 3D culturing system of intestinal organoids (“”miniguts”” in a dish) has been developed. By clonally expanding single intestinal stem cells, we can obtain sufficient DNA to study DNA damage caused by or associated with chronic inflammation. The nature of this DNA damage will serve as a “”smoking gun”” that allows us to identify major forces causing IBD-associated colorectal cancer and thus to develop specific preventive therapies.