Provided herein are compositions, systems, kits, and methods for detecting rejection, or an elevated risk of rejection, of an organ or tissue graft (e.g., kidney graft) in a subject by detecting one, or a panel of, RNA markers in a urine sample from the subject. In certain embodiments, kidney graft injury is detected by measuring one or more of the RNA markers disclosed herein. In some embodiments, the one or more markers are employed to distinguish between acute graft rejection and BK virus nephropathy.