HC is a common complication following HSCT. Risk factors include viral infections, cyclophosphamide and busulfan usage, pelvic irradiation, older age at transplantation, allogeneic HSCT and GvHD. The severity of HC ranges from mild hematuria to life-threatening bleeding. Here, we present a seven-and-a-half-yr-old boy with Wiskott-Aldrich syndrome who experienced a late onset Grade III hemorrhagic cystitis following HSCT from his fully matched sibling. A Grade I GvHD localized to skin developed on day +11 and prednisolone therapy was given between the 11th and 22nd d. Myeloid and platelet engraftments were achieved +13 and +16 d, respectively. A gross hematuria began on the 21st post-transplant day. The urine cultures for bacterial or fungal organisms were negative. Urine analysis by PCR revealed a CMV viruria. Following systemic ganciclovir treatment, urinary CMV became negative but hemorrhagic cystitis did not improve. Due to the probability of existing BK virus or adenovirus, two doses of cidofovir were administered intravesically. As he continued to have painful hematuria with large clot formations, two doses of intravesical hyaluronic acid were applied. Macroscopic hematuria resolved within four d after the second dose. Complete remission was achieved on day +77. Finally, intravesical administration of hyaluronic acid seems to be effective and safe and can be a promising treatment in patients suffering from severe and late onset HC.