The present invention provides novel compositions and methods relating to the treatment of Inflammatory Bowel Disease ("IBD"), most notably, Ulcerative Colitis, Crohn's Disease, Colitis and Diverticulitis. The invention relates to the discovery of a parasitic microsporidia infecting the epithelium cells lining the gastrointestinal tract of patients suffering from IBD. The discovery of this correlation between the disease and the microsporidia, described herein, led to the development of methods for the accurate diagnosis of patients suffering from IBD, and also of methods for treating such a patient in accordance with the invention. This discovery also provides for the development of animal models to further elucidate the mechanism of the disease and potential additional cures therefor. The present invention, in a preferred aspect, provides treatment methods wherein a patient suffering from a microsporidia infection is administered a pharmaceutically-effective amount of a N,N'-di-[halogenated-(lower alkanoyl)]-diamine compound.