Soybean contains a high concentration of carbohydrates that consist mainly of non-starch polysaccharides (NSP) and oligosaccharides. The NSP can be divided into insoluble NSP (mainly cellulose) and soluble NSP (composed mainly of pectic polymers, which are partially soluble in water). Monogastric animals do not have the enzymes to hydrolyze these carbohydrates, and thus their digestion occurs by means of bacterial fermentation. The fermentation of soybean carbohydrates produces short chain fatty acids that can be used as an energy source by animals. The utilization efficiency of the carbohydrates is related to the chemical structure, the level of inclusion in the diet, species and age of the animal. In poultry, soluble NSP can increase digesta viscosity, reduce the digestibility of nutrients and depress growth performance. In growing pigs, these effects, in particular the effect on gut viscosity, are often not so obvious. However, in weaning piglets, it is reported that soy oligosaccharides and soluble NSP can cause detrimental effects on intestinal health. In monogastrics, consideration must be given to the anti-nutritive effect of the NSP on nutrient digestion and absorption on one hand, as well as the potential benefits or detriments of intestinal fermentation products to the host. This mirrors the needs for i) increasing efficiency of utilization of fibrous materials in monogastrics, and ii) the maintenance and improvement of animal health in antibiotic-free production systems, on the other hand. For example, ethanol/water extraction removes the low molecular weight carbohydrate fractions, such as the oligosaccharides and part of the soluble pectins, leaving behind the insoluble fraction of the NSP, which is devoid of anti-nutritive activities. The resultant product is a high quality soy protein concentrate. This paper presents the composition and chemical structures of carbohydrates present in soybeans and discusses their nutritive and anti-nutritive effects on digestion and absorption of nutrients in pigs and poultry.