<i>Background:</i> Since the 1970s a variety of experimental techniques have been employed in an attempt to identify urinary biomarkers of renal injury. While these approaches have met with some success, modern proteomic tools now permit broad based high-throughput analysis of the urinary proteome. <i>Methods:</i> Using the ICAT isotopic labeling based LC/MS/MS approach, comparative urinary protein profiling was performed in a murine model of membranoproliferative glomerulonephritis. Paired samples were analyzed mice with a targeted deletion of the complement regulatory protein factor H (FH^–/–) and control mice. <i>Results:</i> 25 distinct urinary proteins were identified of which 7 were differentially expressed in the FH^–/– mice. Two proteins were markedly altered in the urine of FH^–/– mice compared to controls: uromodulin (5.5-fold lower) and the MHC class II molecule H2^e (8.6-fold higher). Differential expression was confirmed by Western blot and RT-PCR. Immunofluorescent staining demonstrated a marked increased expression of H2^e and a reduction of uromodulin expression in the tubular epithelium of FH^–/– mice. <i>Conclusions:</i> These findings provide insight into early complement-dependent alterations in tubular protein expression which may play critical roles in the development of tubulointerstitial disease, and provide experimental support for the use of urinary proteomic profiling in murine models of renal injury.