Genetic bases of glomerulonephritis, a major cause of kidney dysfunction in humans and one of the most characteristic complications of autoimmune disorders such as Goodpasture syndrome, are complex. The Wistar-Kyoto (WKY) rat strain is well characterized for its susceptibility to autoantibodies against glomerular basement membrane (GBM), however the molecular mechanisms underlining the phenotype are largely unknown. Here we performed a whole genome scan using a backcross (BC) F(1) (WKY x DA) x WKY population, for which the DA rat is a nonsusceptible control strain. We found two significant QTLs on chromosomes 1 and 12, which were involved in elevated levels of proteinuria and kidney weight index, respectively. The relevance of these QTLs with the genetic factors involved in autoimmunity and renal disease is discussed.