Anal fistulas may fail to heal because of continuing disease within the intersphincteric anal glands. Histological studies of the intersphincteric component of 18 consecutive idiopathic anal fistulas show that fistula persistence may be caused by epithelialization of the fistula track from internal or external openings. Some fistulas are lined by epithelium similar to that of anal gland ducts, but this may also represent epithelium derived from the transitional zone of the anal canal. Persistence may be related more to non-specific epithelialization of the track than to a chronically infected anal gland.