The number of microbes associated with our gut likely exceeds our total number of somatic and germ cells. Despite their numbers, almost nothing is known about the molecular mechanisms that determine whether the interaction between a microbial species and its host will be beneficial. Recent results obtained from in vivo models have revealed critical roles for glycoconjugates in helping define the outcome of two such host-microbial relationships. In one case, attachment of Helicobacter pylori to fucosylated or sialylated glycans produced by various gastric epithelial lineages and their progenitors skews the destiny of colonization toward pathogenicity. In the second case, a molecular dissection of how Bacteroides thetaiotaomicron, a normal inhabitant of the distal small intestine, is able to communicate with intestinal epithelial cells has revealed a novel role for host fucosylated glycans in forging a mutually beneficial relationship. These observations lend support to the hypothesis that the capacity to synthesize diverse carbohydrate structures may have arisen in part from our need to both evade pathogenic relationships and to coevolve symbiotic relationships with our nonpathogenic resident microbes.