The present invention relates to methods for preparing high purity gentiooligosaccharides, high purity gentiooligosaccharides obtained therefrom, and uses thereof. The methods of the present invention involve: adding a low purity gentiooligosaccharide to a liquid medium subjecting the liquid medium to inoculation with a microorganism, followed by incubation and fermentation to consume glucose that is contained in the low purity gentiooligosaccharide and subjecting the resulting fermentation broth to filtration and purification. According to the method of the present invention, high purity gentiooligosaccharides having a purity of at least 90% that can be used as alternatives to foods such as cocoa, chocolate, coffee, beer, tea, bread or confectionery product, and beverage or the main ingredients thereof.
