Better characterization of the molecular mechanisms underlying glomerular cell proliferation may improve our understanding of the pathogenesis of glomerulonephritis and yield disease specific markers. We used two dimensional gel electrophoresis (2DE) and mass spectrometry (MS) to generate expression profiles of glomerular proteins in the course of anti Thy 1 nephritis. Glomeruli were isolated from Wistar rats by sieving and proteins were separated by 2DE. In preliminary studies using normal rats, we identified known glomerular proteins from microfilaments (tropomyosin), intermediate filaments (vimentin and lamin A), proteins involved in assembly (alpha actinin-4, F-actin capping protein) and membrane cytoskeletal linking (ezrin) as well as several enzymes (protein disulfide isomerase, ATP synthase and aldehyde dehydrogenase). Comparison of glomerular protein abundance between normal rats and rats in the early phase of anti Thy 1 nephritis yielded 28 differentially expressed protein spots. MS analysis identified 16 differentially expressed proteins including tropomyosin. Altered tropomyosin abundance in the course of anti Thy 1 nephritis was confirmed and specific isoforms were characterized by Western blotting. We demonstrated a complex change in tropomyosin (Tm) isoform abundance in the course of anti Thy 1 nephritis. The early mesangiolytic phase of the disease was characterized by decreased abundance of low molecular weight isoforms Tm5a/5b and increased abundance of high molecular weight isoforms Tm6, Tm1, Tm2 and Tm3. The late proliferative phase of the disease was associated with increased abundance of isoforms Tm 5a/5b, Tm6 and Tm1 and decreased abundance of Tm3. The isoforms Tm4 and Tm5 remained unchanged in the course of this model of experimental glomerulonephritis. Characterization of tropomyosin isoform abundance in the course of clinical glomerulonephritis may identify disease specific markers.