Abstract: Methods and kits for monitoring kidney function, and detecting kidney dysfunction and transplant related disease and rejection are disclosed. The method involves analyzing a sample, such as a urine sample, containing protein from an animal for fragments of ?2-microglobulin, wherein the presence of specific ?2-microglobulin fragments is indicative of kidney dysfunction and transplant rejection. In another embodiement, urine samples from an animal are tested for protease activity, such as cathepsin D or napsin A, wherein increased protease activity compared to a control sample is indicative of kidney dysfunction.