Methods are provided for monitoring a subject having a graft for an acute rejection (AR) response, e.g., to predict, to diagnose, and/or to characterize an AR response. In practicing the subject methods, the expression level of at least one gene in a sample from the subject, e.g., a blood or biopsy sample, is evaluated, e.g., at the nucleic acid and/or protein level, to monitor the subject. Also provided are compositions, systems, kits and computer program products that find use in practicing the subject methods.