In the last years, disease biomarker discovery has highly evolved thanks to the application of high--throughput technologies such as proteomics. However, due to the elevated complexity and abundance of some of the proteins in the samples the analysis of subcellular compartments has been revealed to be fundamental in order to identify underrepresented clinically relevant proteins. In this sense, extracellular microvesicles including exosomes that are present in different body fluids constitute a suitable and convenient subcellular compartment to identify disease biomarkers. On the other hand, animal models offer numerous advantages over human samples in order to accelerate the identification of candidate biomarkers. In this chapter we provide a detailed methodology to purify and analyze urinary exosomes that can be applied to the study of different diseases that have good animal models.