Crohn’s disease (CD) with ulcerative colitis comprises a group of inflammatory bowel diseases. It involves inflammation of the walls of the digestive tract and can affect every part from the mouth to the anus. It is a chronic condition with periods of remission and exacerbation and can often lead to hospitalization and the use of medications and surgery. Based on current literature, it is difficult to clearly determine the causes of CD. Several factors that are involved in molecular pathogenesis have been identified. These include bacterial antigens of the intestinal flora and abnormal immune response, processes responsible for antigen recognition and the balance between T cell subpopulations. As a result of disturbances in the interaction between the intestinal flora and the immune system, local control of inflammation is likely to be lost, which, together with a probable genetic substrate, determines the abnormal immune responses.