Acute allograft rejection is a serious impediment to long-term success in renal transplantation. Early detection of rejection is crucial for treatment of rejection, and can help avoid long-term effects such as chronic rejection or loss of the transplanted organ. The current diagnostic paradigm is a combination of clinical presentation, biochemical measurements (serum creatinine), and needle biopsy. There are significant efforts underway to find alternate biomarkers for early detection of acute rejection, including protein profiling of urine by mass spectrometry. One approach for protein profiling is to use affinity mass spectrometry - we describe a method for this using ProteinChips and SELDI-TOF mass spectrometry.