Exceptionally, gastrointestinal involvement of Churg-Strauss syndrome (CSS) may require extensive bowel resection resulting in a short bowel syndrome. Living related intestinal transplantation (IT) has emerged as an alternative to deceased-donor IT in the management of patients with irreversible short bowel syndrome. Herein, we have presented a 35-year-old patient with isolated intestinal involvement of CSS lesions refractory to steroids and azathioprine requiring multiple abdominal resections resulting in an ultrashort bowel syndrome. A living related IT (from the mother) was performed. She underwent several acute rejection episodes treated with additional immunosuppressive therapy. Despite higher doses of immunosuppression, these repeated acute rejection episodes eventually evolved into a syndrome of chronic allograft rejection. Eventually, owing to her poor general condition and to avoid life-threatening infections, transplantectomy was inevitable. Recent immunologic studies indicate that peripheral mononuclear cells from patients with CSS secrete large amounts of T-helper type 1 and 2 cytokines. It is likely that patients with CSS are at higher risk for acute and chronic rejection after transplantation.