The capability of the noncollagenous (NC1) domains of the six alpha chains of human type IV collagen to induce anti-glomerular basement membrane (GBM) nephritis in WKY rats was determined. This was accomplished by using recombinant technology to express the six NC1 domains in mammalian 293 cells and to purify the proteins using an anti-Flag affinity column. All rats injected with alpha 3(IV)NC1 and alpha 4(IV)NC1 developed proteinuria and hematuria. Rats injected with alpha 5(IV)NC1 developed mild hematuria, whereas rats injected with the alpha 1(IV)NC1, alpha 2(IV)NC1 and alpha 6(IV)NC1 domains developed neither proteinuria nor hematuria. The renal lesions induced by alpha 3(IV)NC1 and alpha 4(IV)NC1 domains were characteristic of those in patients with anti-GBM nephritis and Goodpasture syndrome. The experimental nephritis is mediated by anti-basement membrane antibodies that are targeted to alpha 3(IV)NC1 and alpha 4(IV)NC1 domains and which bind to the glomerular basement membrane. The uniqueness of the alpha 3(IV)NC1 and alpha 4(IV)NC1 domains, among the six NC1 domains, to induce severe anti-GBM disease may relate to the accessibility of epitopes in the GBM for binding of antibody. The pathogenicity of the alpha 4(IV)NC1 antibodies establishes a conundrum because the pathogenic antibodies in patients are not targeted to the alpha 4(IV)NC1, but are targeted to the alpha 3(IV)NC1 domain in anti-GBM nephritis and to the alpha 3(IV)NC1 and alpha 5(IV)NC1 domains in Alport post-transplant anti-GBM nephritis.