Matrix stones are radiolucent bodies that present as soft muco-proteinaceous material within the renal collecting system. Following wide-angle X-ray diffraction (XRD) and scanning electron microscopy (SEM), we homogenized a surgically removed matrix stone, extracted and purified protein, and analyzed samples using tandem mass spectrometry for proteomic composition. Resulting spectra were searched using ProteinPilot 2.0, and identified proteins were reported with >95% confidence. Primary XRD mineral analysis was a biological apatite, and SEM revealed fibrous, net-like laminations containing bacterial, cellular, and crystalline material. Of the 33 unique proteins identified, 90% have not been previously reported within matrix stones and over 70% may be considered inflammatory or defensive in nature. Characterization of other matrix stone proteomes, in particular from non-infectious populations, may yield insights into the pathogenesis of this rare stone as well as the mineralogical process that occurs within crystalline calculi.