Membranous nephropathy (MN), a common cause of idiopathic nephrotic syndrome in adults, remains a potentially devastating problem worldwide. At present, there is no reliable noninvasive method for predicting and/or monitoring this glomerular disease, and its pathophysiology remains poorly understood. In the present study, the urinary proteome profile of rats after 10 days of an induction of passive Heymann nephritis (PHN), which resembles human MN, was compared to that of the baseline (control) urine prior to the induction of PHN by anti-Fx1A injection. Each pool of PHN and control urine samples (n = 10 each) was labeled with different fluorescent dyes (Cy3 or Cy5), and equal amounts of the labeled proteins of both pools were resolved in the same 2D gel, together with an internal standard labeled with Cy2. Two-dimensional difference gel electrophoresis revealed a number of protein spots whose expression levels were altered during PHN. Eighteen protein spots with >1.5-fold changes and p < 0.05 were selected for subsequent identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. They were successfully identified as serum albumin precursor, alpha-1-antitrypsin, preprohaptoglobin, liver-regeneration-related protein, and transthyretin (which increased during PHN) and E-cadherin, MPP7, tropomyosin beta, kallikrein, and alpha-2u globulin (which decreased in the PHN urine). Among these proteins, the increase in urinary preprohaptoglobin has particularly drawn our attention because of its byproduct, haptoglobin (Hp), which is involved in the protection of tissue damage from hemoglobin-induced oxidative stress. Western blotting and enzyme-linked immunosorbent assay clearly showed a markedly increased level of Hp in the urine, but not in the serum, of the PHN animals. Our findings may lead to a significant advance in the attempt to define a new therapeutic target and/or novel biomarker for human MN.