Microbiota in the gut play essential roles in human health. Prebiotics are non-digestible complex carbohydrates that are fermented in the colon, yielding energy and short chain fatty acids, and selectively promote the growth of Bifidobacteria and Lactobacillae in the gastro-intestinal tract. Fructans and inulin are the best-characterized plant prebiotics. Many vegetable, root and tuber crops as well as some fruit crops are the best-known sources of prebiotic carbohydrates, while the prebiotic-rich grain crops include barley, chickpea, lentil, lupin, and wheat. Some prebiotic-rich crop germplasm have been reported in barley, chickpea, lentil, wheat, yacon, and Jerusalem artichoke. A few major quantitative trait loci and gene-based markers associated with high fructan are known in wheat. More targeted search in genebanks using reduced subsets (representing diversity in germplasm) is needed to identify accessions with prebiotic carbohydrates. Transgenic maize, potato and sugarcane with high fructan, with no adverse effects on plant development, have been bred, which suggests that it is feasible to introduce fructan biosynthesis pathways in crops to produce health-imparting prebiotics. Developing prebiotic-rich and super nutritious crops will alleviate the widespread malnutrition and promote human health. A paradigm shift in breeding program is needed to achieve this goal and to ensure that newly-bred crop cultivars are nutritious, safe and health promoting.