Alport post-transplant nephritis (APTN) is an aggressive form of anti-glomerular basement membrane disease that targets the allograft in transplanted patients with X-linked Alport syndrome. Alloantibodies develop against the NC1 domain of a5(IV) collagen, which occurs in normal kidneys, including renal allografts, forming distinct a345(IV) and a1256(IV) networks. Here, we studied the roles of these networks as antigens inciting alloimmunity and as targets of nephritogenic alloantibodies in APTN. We found that patients with APTN, but not those without nephritis, produce two kinds of alloantibodies against allogeneic collagen IV. Some alloantibodies targeted alloepitopes within a5NC1 monomers, shared by a345NC1 and a1256NC1 hexamers. Other alloantibodies specifically targeted alloepitopes that depended on the quaternary structure of a345NC1 hexamers. In Col4a5-null mice, immunization with native forms of allogeneic collagen IV exclusively elicited antibodies to quaternary a345NC1 alloepitopes, whereas alloimmunogens lacking native quaternary structure elicited antibodies to shared a5NC1 alloepitopes. These results imply that quaternary epitopes within a345NC1 hexamers may initiate alloimmune responses after transplant in X-linked Alport patients. Thus, a345NC1 hexamers are the culprit alloantigen and primary target of all alloantibodies mediating APTN, whereas a1256NC1 hexamers become secondary targets of antia5NC1 alloantibodies. Reliable detection of alloantibodies by immunoassays using a345NC1 hexamers may improve outcomes by facilitating early, accurate diagnosis.