In IgA nephropathy (IgAN), there is dysregulation of the IgA response to a wide range of antigens. The dysregulation promotes synthesis of polymeric IgA1 (pIgA1) with physicochemical characteristics that favor mesangial deposition, including altered O-glycosylation of the hinge region. This may be the synthesis of IgA in the systemic compartment, which has the phenotype of mucosal IgA. There is not a change in IgA1 structure to an entirely abnormal form; rather, there is a shift that results in a proportional increase in forms of IgA1 also found in healthy individuals. Altered O-glycosylation could favor pIgA1 deposition by promoting formation of macromolecular IgA and immune complexes. Mesangial injury follows through interactions of pIgA1 with the cells and extracellular matrix proteins of the mesangium and the activation of complement. The final clinical expression of IgAN also depends on generic factors, including hypertension and proteinuria, and a fibrotic renal response. No single "IgAN gene" has been identified, and it is likely that multiple interacting genes will eventually prove to underlie susceptibility to IgAN and the risk of progressive renal disease. These new pathogenic insights have not yet led to new therapeutic opportunities.