Previous research has revealed that waxy corn starch which has been entrapped in a matrix of electrostatically cross-linked alginate, shows a slow digestion rate such that much of the starch may reach the colon; thus making this a new type of resistant starch. The purpose of this research was to test the fermentative properties of starch-entrapped microspheres using a batch fecal fermentation method. Fermentation of starch-entrapped microspheres showed significantly lower rates of gas production compared to waxy corn starch, and showed significant increases in total SCFAs during the latter stages of fermentation (24-48 h), whereas waxy corn starch did not. Cooking the starch-entrapped microspheres increased the amount of SCFAs and the molar fraction of butyrate produced during fermentation. Bacterial fingerprinting revealed that uncooked starch-entrapped microspheres have a unique effect on the microbiota that is different from waxy corn starch alone, but cooking causes a shift toward a pattern more closely resembling that of the starch. Starch-entrapped microspheres may deliver slowly fermentable carbohydrate to the colon, with the ability to influence the microbiota. Further human studies are required to determine whether these characteristics occur in vivo.