A major goal of clinical proteomics was to identify biomarkers that can aid in the diagnosis and prognosis of different conditions. These biomarkers will not only assist the clinician in the diagnosis of a disease but they will also give directions as to which therapy may be more appropriate for each patient, thus contributing to the development of personalized medicine. This review discusses the current concepts in urine proteomics aimed at identifying predictive biomarkers that could detect the presence of acute rejection or chronic allograft dysfunction early on and for instance be used to personalize immunosuppressive therapies for kidney transplant patients.