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IgA nephropathy is defined by the presence of IgA-dominant or co-dominant immune deposits within glomeruli. Biopsy specimens meeting these diagnostic criteria have a range of histological changes that are reflected in the variable clinical course of IgA nephropathy. The impact of histology on outcomes in IgA nephropathy has been clarified in a number of large retrospective clinicopathological studies. These studies have consistently demonstrated that the stage of disease at presentation, as indicated by the extent of interstitial fibrosis and tubular atrophy in the biopsy, is the strongest histological predictor of renal survival. The effect of active proliferative lesions on the disease course is less clear cut, owing in part to considerable treatment bias in most published retrospective studies. There is evidence that endocapillary hypercellularity and cellular crescents are responsive to immunosuppressive therapy, but this observation requires confirmation in prospective randomized controlled trials. Future challenges include improving the reproducibility of histological scoring, particularly for the presence and extent of endocapillary lesions, and to improve prognostic modelling by combining histological data with clinical variables and biomarker data.