Inflammatory bowel diseases (IBDs), such as Crohn's disease (CD), involve a poorly understood and complex immune response to both the biota of the human gut and the gut itself. The role of the gut biota in human health has been ill defined and attitudes toward the intestinal flora have ranged from judging them largely irrelevant to declaring them a human organ system. A better way to view the intestinal flora is as a group of evolutionarily self-interested species that form large, potentially interbreeding populations that utilize human beings as a series of semi-isolated habitats, like islands in an archipelago. Here we propose that the imposition of modern sanitation and hygiene standards has drastically attenuated the connection between the “islands” inhabited by the gut flora, and that existing work drawn from evolutionary biology studies of island ecosystems, rather than medicine, predicts that the evolution of gut flora should now be pushed toward limited-dispersion forms of intestinal microorganisms – a proposition borne out by the discovery of so-called “adherent invasive Escherichia coli.” This pathogenic variant of the gut bacterium E. coli clings to and invades the intestinal epithelium and has been implicated in CD. Gut flora and diseases of the gut should arguably be studied as ecology as much as medicine, and treated within this context.