Biomarkers are the monitorable changes associated with physiological or pathological changes. Urine is not regulated by the homeostatic mechanism and can reflect multiple changes in the body. Animal models can simulate human disease processes, monitor disease changes, and provide clues for early diagnosis. In this chapter, clues are provided for the dominant model animals associated with disease selection by comparing the urine proteome of rats, guinea pigs, and golden hamsters. The peptides were cleaved by membrane digestion and analyzed by LC-MS/MS. The number of urine proteins in the three different animals was different, and also different in every system of the body. This provides a basis for selecting the best animal models for different diseases.