The most well-known food-based strategies to modulate the composition of the intestinal microbiota are the dietary use of prebiotics, probiotics, and their combination, synbiotics. Currently established prebiotic compounds are mainly targeting the bifidobacteria population of the colon microbiota. A good illustration of the importance of high colonic bifidobacteria levels is the observation that breast milk creates an environment in the colon (because of its high amount in galacto-oligosaccharides with prebiotic activity) favoring the development of a simple flora, dominated by bifidobacteria to which various health benefits have been ascribed. Currently, high colonic bifidobacteria levels have been considered favorably at all ages, and strategies to augment their presence have been demonstrated in placebo-controlled intervention studies; e.g. in toddlers to reduce sickness events, in adults to reduce the risk for developing gastrointestinal diseases and in the elderly to re-enhance their declining immune activity. The intestinal microbiota can be considered as a metabolically adaptable and rapidly renewable organ of the body. However, unbalances in its microbial community and activities are found to be implicated in disease initiation and progression, such as chronic inflammatory bowel diseases and colonic cancers. Restoration of this balance by increasing bifidobacteria levels has been demonstrated to reduce the disease severity of patients and to improve well-being in healthy volunteers. New emerging evidence on the difference in the composition of the colonic microbiota between obese and lean volunteers has opened new areas for pre-, pro-and synbiotic research. Additionally, as knowledge will increase about the microbial bio-conversion of polyphenolic compounds into bioactive metabolites in the colon and whether food-based strategies can augment such bioconversion into more potent compounds with anti-oxidant and/or anti-inflammatory activity new areas of research will be discovered. This paper provides an up-to-date review of the health benefits associated with the induction of high bifidobacteria levels in the colon by the use of prebiotics (inulin and oligofructose). New areas of emerging science will be discussed as well.