Methods and compositions for treating diseased or damaged tissue, such as Inflammatory Bowel Disease, e.g., Ulcerative Colitis, include tissue regeneration using stem cells or tissue grafts which stimulate stem cell migration to the damaged tissue. The tissue grafts can be extracellular matrix (ECM) material, such as tissue-specific extracellular matrix (TS-ECM). The methods can also include mucosal resection of the damaged or diseased tissue prior to placement of the graft.