In general, the invention is directed to treatment of fecal incontinence by the implantation of one or more bulking prostheses proximate to an anal sphincter. These bulking prostheses, which may include biocompatible hydrogel, are inserted into the tissue near the anus through a small opening in the mucosa. When inserted, the bulking prostheses are in a miniature state. Upon introduction into the body, the devices enter an enlarged state. In their enlarged state, the bulking prostheses supply extra bulk to the tissues proximate to the anal sphincters. With the extra bulk, the patient can exercise voluntary control over the external sphincter to close the anus and maintain fecal continence.