Despite all the advances in our understanding of the pathophysiology of inflammatory bowel disease (IBD), we do not know the cause. Some of the most recently available data have been discussed here and yet it is now becoming increasingly accepted that immunogenetics play an important role in the predisposition, modulation, and perpetuation of IBD. The mucosal immune system is the central effector of intestinal inflammation and injury, with cytokines playing a central role in modulating inflammation. The role of intestinal milium, and enteric flora in particular, appears to be of greater significance than previously held. A review is made of the main areas of research exploring the mechanisms more intimately associated with the development of IBD, providing advances in the agents currently used, and identifying a host of new therapeutic agents potentially interacting with or interrupting specific targets in the genesis of IBD.