Viral infections represent severe complications in immunodeficient patients, associated with significant morbidity and mortality. We report a case of a bone marrow-transplanted adolescent with hemorrhagic cystitis 4 weeks after transplant, associated with renal failure because of obstructive pyelonephritis. Diagnostic workup finally revealed adenovirus infection. A double-J stent was inserted with spontaneous favorable evolution thereafter. Adenovirus infection in an immunocompromised patient can cause hemorrhagic cystitis without specific symptoms and might evolve toward obstructive pyelonephritis because of tubular necrosis. Diagnosis is made by urine culture and/or blood polymerase chain reaction. In case of fatal dissemination, diagnosis might only be revealed on autopsy.