The concept of colonic health has become a major target for the development of functional foods such as probiotics, prebiotics, and synbiotics. These bioactive agents have a profound effect on the composition of the microflora, as well as on the physiology of the colon, and display distinct health benefits. Dietary carbohydrates escaping digestion/absorption in the small bowel and prebiotics undergo fermentation in the colon and give rise to short-chain fatty acids (SCFA). As the main anions of the colon and the major source of energy for colonocytes, SCFA are rapidly absorbed by nonionic diffusion mostly but also by active transport mediated by a sodium-coupled transporter, thereby fostering the absorption of sodium and water. SCFA in general and butyrate in particular enhance the growth of lactobacilli and bifidobacteria and play a central role on the physiology and metabolism of the colon. The effect of prebiotics on cell proliferation, differentiation, apoptosis, mucin production, immune function, mineral absorption, lipid metabolism, and gastrointestinal (GI) peptides has been well documented experimentally. These effects seem to be largely mediated by SCFA, but evidence from human studies remains inconsistent. The food industry is making a leap of faith in their efforts to commercialize prebiotics and exploit potential health benefits. The future lies with the design of studies to further explore basic mechanisms, and gene expression in particular, but emphasis should be placed on human intervention trials.